From 32613662dfbd6c50662f7c7bab1a0578c5b0b2f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:29:47 +0100 Subject: [PATCH 0001/2403] add easyconfig file for Extrae --- .../Extrae-2.4.1-gompi-1.5.12-no-OFED.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..bcb4f32de9 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,63 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Extrae" +version = "2.4.1" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22', "", (compname, compver)), + ('Boost', '1.53.0', '-serial', (compname, compver)), + ('libunwind', '1.1', "", (compname, compver)), + ('libxml2', '2.9.1', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +configopts = ' --with-mpi=${EBROOTOPENMPI}' +configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' +configopts += ' --enable-xml --enable-merge-in-trace' +configopts += ' --with-unwind=${EBROOTLIBUNWIND}' +configopts += ' --without-dwarf --without-dyninst' +configopts += ' --with-boost=${EBROOTBOOST}' +# --- BM ISSUE --- +# +# Does not build with EasyChair provided binutils (libbfd/liberty not shared/compiler with -fPIC) +#configopts += ' --with-binutils=${EBROOTBINUTILS}' + +# --- BM EXTENSIONS --- +# +# Extrae also supports CUDA measurements - not yet tested +# configopts ++ ' --with-cuda=${CUDADIR} --with-cupti=${CUDADIR}/extras/CUPTI' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/mpi2prv", "include/extrae_user_events.h", "lib64/libmpitrace.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From 87c41fc3fc9c005442ea8cd976bdb602b9eb8f8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:32:22 +0100 Subject: [PATCH 0002/2403] add easyconfig file for Paraver --- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb new file mode 100644 index 0000000000..d62b7707a8 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -0,0 +1,70 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Paraver" +version = "4.4.5" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +dependencies = [ + ('wxPropertyGrid', '1.4.15'), + ('Boost', '1.53.0', '-serial'), +] + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] + +# --- BM ISSUE --- +# +# lib64/lib linking should be avoided by patching Paraver configure/Makefiles files +# configure/Makefile assumes everything always in lib/ +preconfigopts = [ + 'cd ptools_common_files; ', + 'ln -s -f %(installdir)s/ptools/lib64 %(installdir)s/ptools/lib; cd paraver-kernel; ', + 'ln -s -f %(installdir)s/lib64 %(installdir)s/lib; cd wxparaver;' +] +premakeopts = [ + 'cd ptools_common_files; ', + 'cd paraver-kernel; ', + 'cd wxparaver;' +] +preinstallopts = [ + 'cd ptools_common_files; ', + 'cd paraver-kernel; ', + 'cd wxparaver;' +] + +configopts = [ + '--prefix=%(installdir)s/ptools', + '--with-boost=${EBROOTBOOST}' + + ' --with-ptools-common-files=%(installdir)s/ptools', + '--with-boost=${EBROOTBOOST}' + + ' --with-wxpropgrid=wxcode_gtk2_propgrid-2.8' + + ' --with-paraver=%(installdir)s' +] + +keeppreviousinstall = True + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/wxparaver", "include/paraverconfig.h", + "lib64/paraver-kernel/libparaver-kernel.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From fe8a6dcbd0ee0ff9222e528d105c840797b87d80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:33:39 +0100 Subject: [PATCH 0003/2403] add easyconfig file for TAU --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 114 ++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..bda1e46477 --- /dev/null +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,114 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +import platform + +name = "TAU" +version = "2.22.2" +# --- BM ISSUE --- +# +# Use hardcoded x86_64 here? +machine = platform.machine() + +homepage = 'http://tau.uoregon.edu' +description = """The TAU Performance System is a portable profiling and tracing toolkit + for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('OTF', '1.12.4', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), + ('PDT', '3.19', "", (compname, compver)), + ('Scalasca', '1.4.3'), + ('Score-P', '1.2.1'), + ('VampirTrace', '5.14.4'), +] + +# http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] + +# --- BM CONFIGOPTS --- +# +# Compiler should always be specified -- MUCH quicker and SAVER than autodetect +# -c++=[CC|KCC|g++|*xlC*|cxx|pgCC|pgcpp|FCC|guidec++|aCC|c++|ecpc| +# clang++|bgclang++|g++4|icpc|scgcc|scpathCC|pathCC|orCC] +# -cc=[cc|gcc|clang|bgclang|gcc4|scgcc|KCC|pgcc|guidec|*xlc*|ecc|pathcc|orcc] +# -fortran=[gnu|sgi|ibm|ibm64|hp|cray|pgi|absoft|fujitsu|sun|compaq|g95| +# open64|kai|nec|hitachi|intel|absoft|lahey|nagware|pathscale|gfortran|gfortran4] + +# Basic config: compiler, OpenMP, MPI +compcfgopts = ' -cc=gcc -c++=g++ -fortran=gfortran4' +ompcfgopts = ' -opari' +mpicfgopts = ' -mpiinc=${EBROOTOPENMPI}/include -mpilib=${EBROOTOPENMPI}/lib64' + +# Optional extra modes config: +scacfgopts = ' -scalasca=${EBROOTSCALASCA}' +vtcfgopts = ' -vampirtrace=${EBROOTVAMPIRTRACE}' +scocfgopts = ' -scorep=${EBROOTSCOREMINP}' + +# Optional packages config: +pdtcfgopts = ' -pdt=${EBROOTPDT}' +papicfgopts = ' -papi=${EBROOTPAPI}' +optionalcfgs = pdtcfgopts + papicfgopts # + otfcfgopts +# --- BM ISSUE --- +# +# TAU cannot handle name changes yet introduced with OTF-1.12.3 +#otfcfgopts = ' -otf=${EBROOTOTF}' + +# TAU special build procedure +prefix_opt = '-prefix=' +installopts = 'clean' +keeppreviousinstall = True +skipsteps = ['build'] + +# TAU build: Configure + make install for each combination of modes defined above +configopts = [ + # Basic TAU mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+optionalcfgs, + compcfgopts+ompcfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+optionalcfgs, + # Scalasca mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+scacfgopts+optionalcfgs, + compcfgopts+ompcfgopts+scacfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+scacfgopts+optionalcfgs, + # Vampirtrace mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+vtcfgopts+optionalcfgs, + compcfgopts+ompcfgopts+vtcfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+vtcfgopts+optionalcfgs, + # Score-P mode + MPI, OMP, OMPI + compcfgopts+mpicfgopts+scocfgopts+optionalcfgs, + compcfgopts+ompcfgopts+scocfgopts+optionalcfgs, + compcfgopts+mpicfgopts+ompcfgopts+scocfgopts+optionalcfgs, +] + +sanity_check_paths = { + 'files': [machine + "/bin/pprof", "include/TAU.h", machine + "/lib/libTAU.so"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': machine + "/bin", + 'TAU_MF_DIR': machine + "/lib", + 'TAU_MAKEFILE': machine + "/lib/Makefile.tau-papi-mpi-pdt", +} +modextravars = { + 'TAU_PROFILE': '1', + 'TAU_TRACE': '0', + 'TAU_CALLPATH': '1', + 'TAU_CALLPATH_DEPTH': '10', + 'TAU_COMM_MATRIX': '1', +} + +moduleclass = 'perf' -- GitLab From c55d537bdc983511d29966d67e4698ba56b75682 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:35:53 +0100 Subject: [PATCH 0004/2403] add easyconfig file for VampirTrace --- ...VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..304ad188de --- /dev/null +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb @@ -0,0 +1,72 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "VampirTrace" +version = "5.14.4" + +homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' +description = """VampirTrace is an open source library that allows detailed logging of program + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). + Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated + applications and generates exact time stamps for all GPU related events. + Additional highlights are I/O event and memory allocation tracing as well as recording of counter metrics + like PAPI and external counters. + VampirTrace provides several variants to instrument the application source code, such as manual, automatic + by the compiler, binary (Dyninst) instrumentation and library wrapping. + The log data is written in the Open Trace Format (OTF), which can be analyzed and visualized by the visualization tool Vampir. + VampirTrace has established a wide user base and has become an integral part of Open MPI version 1.3 and higher.""" + +toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.7.3' + +# compiler toolchain depencies +dependencies = [ + ('OTF', '1.12.4', "", (compname, compver)), + ('PAPI', '5.2.0', "", (compname, compver)), + ('PDT', '3.19', "", (compname, compver)), +] + +# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] + +# --- BM CONFIGOPTS --- +# +# MPI suite should always be specified -- MUCH quicker and SAVER than autodetect +# --with-hpmpi | --with-pcmpi | --with-intelmpi | --with-intelmpi2 | --with-lam | --with-mpibgl | --with-mpibgp | +# --with-mpibgq | --with-mpich | --with-mpich2 | --with-mvapich | --with-mvapich2 | --with-mpisx | --with-mpisx-ew | +# --with-openmpi | --with-openmpi17 | --with-sgimpt | --with-sunmpi | --with-sunmpi-mt | --with-mpibull2 +# +# --- BM ISSUE --- +# +# MPIxx variable settings and --enable-compinst= options are ToolChain specific!!! +configopts = ' MPIFC=mpif90' +configopts += ' --with-openmpi' # quicker and saver than autodetect +configopts += ' --enable-compinst=gnu' +configopts += ' --with-papi-dir=${EBROOTPAPI}' +configopts += ' --with-extern-otf-dir=${EBROOTOTF}' +configopts += ' --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor' +configopts += ' --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse' +configopts += ' --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse' +configopts += ' --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse' +# --- BM EXTENSIONS --- +# +# VamoirTrace does also support CUDA measurements - not yet tested in EasyBuild +# configopts += ' --with-cuda-dir=${CUDADIR}' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ["bin/vtcc", "include/vampirtrace/vt_user.h", "lib64/libvt.a"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From 21b39b1378d0f4692026b3cbd3a155c63395476b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:39:07 +0100 Subject: [PATCH 0005/2403] add libunwind, libxml2 easyconfigs as deps for Extrae --- .../l/libunwind/libunwind-1.1-GCC-4.7.3.eb | 33 +++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb | 35 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..14a732a78d --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of this project is to define a portable and efficient C + programming interface (API) to determine the call-chain of a program. The API + additionally provides the means to manipulate the preserved (callee-saved) state of each + call-frame and to resume execution at any point in the call-chain (non-local goto). + The API supports both local (same-process) and remote (across-process) operation.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +# http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib64/libunwind.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..fd7840cbe9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +# --- BM LIB64 --- +# +# On some systems libraries end up in lib/ +sanity_check_paths = { + 'files': ['include/libxml2/libxml/SAX2.h', 'lib64/libxml2.a'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 78c0ed0d951054b835bfa17131dea4b54fc2061b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:42:32 +0100 Subject: [PATCH 0006/2403] add Boost easyconfig as dependency for Paraver --- .../b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb new file mode 100644 index 0000000000..98fbdcdb13 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb @@ -0,0 +1,20 @@ +name = 'Boost' +version = '1.53.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 6665eb9369001333f58db7ae70e2bbcad28b5bf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:44:21 +0100 Subject: [PATCH 0007/2403] add wxPropertyGrid easyconfig as dependency for Paraver --- .../wxPropertyGrid-1.4.15-GCC-4.7.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb new file mode 100644 index 0000000000..859fce3a0d --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "wxPropertyGrid" +version = "1.4.15" + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ["include/wx/propgrid/propgrid.h", "lib64/libwxcode_gtk2_propgrid-2.8.so"], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' -- GitLab From 270485a504f4690b9d91d159ce6a7ed9fec37b53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:41:22 +0100 Subject: [PATCH 0008/2403] redefine Extrae easyconfigs on top of gompi/1.4.12-no-OFED toolchain --- ....eb => Extrae-2.4.1-gompi-1.4.12-no-OFED.eb} | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/e/Extrae/{Extrae-2.4.1-gompi-1.5.12-no-OFED.eb => Extrae-2.4.1-gompi-1.4.12-no-OFED.eb} (82%) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb similarity index 82% rename from easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index bcb4f32de9..c17e508f12 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -17,19 +17,16 @@ description = """Extrae is the core instrumentation package developed by the Per code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} -compname = 'GCC' -compver = '4.7.3' - # compiler toolchain depencies dependencies = [ - ('binutils', '2.22', "", (compname, compver)), - ('Boost', '1.53.0', '-serial', (compname, compver)), - ('libunwind', '1.1', "", (compname, compver)), - ('libxml2', '2.9.1', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), + ('binutils', '2.22'), + ('Boost', '1.53.0'), + ('libunwind', '1.1'), + ('libxml2', '2.9.1'), + ('PAPI', '5.2.0'), ] # http://www.bsc.es/computer-sciences/performance-tools/downloads @@ -44,7 +41,7 @@ configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' # --- BM ISSUE --- # -# Does not build with EasyChair provided binutils (libbfd/liberty not shared/compiler with -fPIC) +# Does not build with EasyBuild provided binutils (libbfd/liberty not shared/compiler with -fPIC) #configopts += ' --with-binutils=${EBROOTBINUTILS}' # --- BM EXTENSIONS --- -- GitLab From 025aff3519f23bd7e61c43bee4e2fee6b8338cba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:43:26 +0100 Subject: [PATCH 0009/2403] redefine libunwind and libxml2-2.9.1 GCC easyconfigs for gompi/1.4.12-no-OFED toolchain --- ...-1.1-GCC-4.7.3.eb => libunwind-1.1-gompi-1.4.12-no-OFED.eb} | 2 +- ....9.1-GCC-4.7.3.eb => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libunwind/{libunwind-1.1-GCC-4.7.3.eb => libunwind-1.1-gompi-1.4.12-no-OFED.eb} (95%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.7.3.eb => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} (94%) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb similarity index 95% rename from easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb rename to easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 14a732a78d..5406346b58 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -16,7 +16,7 @@ description = """The primary goal of this project is to define a portable and ef call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation.""" -toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} # http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index fd7840cbe9..de3b30363f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -7,6 +7,7 @@ # http://apps.fz-juelich.de/unite/ ## easyblock = 'ConfigureMake' + name = 'libxml2' version = '2.9.1' @@ -14,7 +15,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ 'http://xmlsoft.org/sources/', -- GitLab From 919c6a212f20ccff681083a5502ad9651b9136db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Nov 2013 23:45:38 +0100 Subject: [PATCH 0010/2403] add Boost easyconfig required for Extrae --- .../Boost-1.53.0-gompi-1.4.12-no-OFED.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..3e994ae064 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' -- GitLab From 6a71b3ac644fe5d4d45087c7b02ee1bfc0238811 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 19:05:30 +0100 Subject: [PATCH 0011/2403] add alternative lib path for libunwind --- .../l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 5406346b58..5a47aa7676 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -26,7 +26,7 @@ source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] # # On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ['include/libunwind.h', 'lib64/libunwind.a'], + 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], 'dirs': [], } -- GitLab From 0da7ae12501255618ba7371e674aaa710f9783e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 19:18:02 +0100 Subject: [PATCH 0012/2403] tweak sanity check paths for libxml2 consistently, provide alternative paths for libraries --- .../libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 5 +++++ .../libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 5 +++++ .../libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 5 +++++ .../libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 15 ++------------- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 5 +++++ 15 files changed, 72 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index c67963ba18..3d078ed6cf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index 3d1f3f2077..d35a5afd09 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index c92bb71719..111dd07ee9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 1a06b1ab67..8718a3c0cd 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 1babda58a0..5f8aa9158f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index 9c2538dce1..df4be8cc11 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 34aa5f2ec6..ddb04fedc9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 59de5c01a7..2d7551a78a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index 5618053aba..f6b392b5e3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index 0d54f03977..d743e7f4c4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index de3b30363f..6f75ccd50e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,3 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# License:: New BSD -# -# This work is based from experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## easyblock = 'ConfigureMake' name = 'libxml2' @@ -25,12 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ['include/libxml2/libxml/SAX2.h', 'lib64/libxml2.a'], - 'dirs': [], + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index b46d67c8c8..35fadff4ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 02c5f8e418..51cf5a1ff9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index b3eac90a51..28520b4f81 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e18bbcef3b..d80e534ea6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' -- GitLab From bc2b6e49e59174bf38b059fc3da70e78f521c5a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Nov 2013 21:44:26 +0100 Subject: [PATCH 0013/2403] add lib alternative in Extrae sanity check --- .../easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index c17e508f12..0737ca7b22 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -53,7 +53,7 @@ configopts += ' --with-boost=${EBROOTBOOST}' # # On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ["bin/mpi2prv", "include/extrae_user_events.h", "lib64/libmpitrace.a"], + 'files': ["bin/mpi2prv", "include/extrae_user_events.h", ("lib64/libmpitrace.a", "lib/libmpitrace.a")], 'dirs': [] } -- GitLab From 3e0004f2542bc99af0a43dc52f1b90a4fec5f5a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Nov 2013 17:13:35 +0100 Subject: [PATCH 0014/2403] enable -fPIC for binutils, add gompi easyconfig for binutils as dependency for Extrae --- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 8 +++-- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 33 +++++++++++++++++++ .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 7 ++-- 3 files changed, 42 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index cdbab8b742..add5f24592 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -20,12 +20,14 @@ sources = ['binutils-%s.tar.bz2' % version] source_urls = ['http://ftp.gnu.org/gnu/binutils'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist], - 'dirs': [] - } + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..17866810c4 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +name = 'binutils' +version = '2.22' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils-2.22: GNU binary utilities" + +sources = ['binutils-%s.tar.bz2' % version] +source_urls = ['http://ftp.gnu.org/gnu/binutils'] + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index aa4cc4cdb0..9ccfe20342 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -24,8 +24,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist], - 'dirs': [] - } + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} moduleclass = 'tools' -- GitLab From 8adc0744b3c9bbfdfe0eb90759cad3d253445b57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Nov 2013 17:18:50 +0100 Subject: [PATCH 0015/2403] make sure Extrae pick up the right libbfd.a and libiberty.a libraries by patching configure and tweaking $LDFLAGS --- ...a-2.4.1_configure-no-shared-binutils.patch | 14 ++++++++++++ .../Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 22 +++++++++---------- 2 files changed, 24 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch diff --git a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch new file mode 100644 index 0000000000..8b712760c3 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch @@ -0,0 +1,14 @@ +--- configure.orig 2013-11-11 16:38:11.872367495 +0100 ++++ configure 2013-11-11 16:38:32.872767289 +0100 +@@ -27477,9 +27477,9 @@ + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" + elif test -r "${binutils_home_dir}/lib/libbfd.so" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" +- elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a"; then #-a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" +- elif test -r "${binutils_home_dir}/lib/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib/libbfd.a"; then # -a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" + else + if test -d ${binutils_home_dir}/lib${BITS} ; then diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index 0737ca7b22..d8500be6ba 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -20,6 +20,12 @@ description = """Extrae is the core instrumentation package developed by the Per toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['Extra-2.4.1_configure-no-shared-binutils.patch'] + # compiler toolchain depencies dependencies = [ ('binutils', '2.22'), @@ -29,29 +35,21 @@ dependencies = [ ('PAPI', '5.2.0'), ] -# http://www.bsc.es/computer-sciences/performance-tools/downloads -# Requires input of email address for download -sources = [SOURCELOWER_TAR_BZ2] - configopts = ' --with-mpi=${EBROOTOPENMPI}' configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' configopts += ' --enable-xml --enable-merge-in-trace' configopts += ' --with-unwind=${EBROOTLIBUNWIND}' configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' -# --- BM ISSUE --- -# -# Does not build with EasyBuild provided binutils (libbfd/liberty not shared/compiler with -fPIC) -#configopts += ' --with-binutils=${EBROOTBINUTILS}' +configopts += ' --with-binutils=${EBROOTBINUTILS}' +# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC +preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' # --- BM EXTENSIONS --- # # Extrae also supports CUDA measurements - not yet tested -# configopts ++ ' --with-cuda=${CUDADIR} --with-cupti=${CUDADIR}/extras/CUPTI' +# configopts += ' --with-cuda=${EBROOTCUDA} --with-cupti=${EBROOTCUDA}/extras/CUPTI' -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { 'files': ["bin/mpi2prv", "include/extrae_user_events.h", ("lib64/libmpitrace.a", "lib/libmpitrace.a")], 'dirs': [] -- GitLab From 25250ead1ae49ce4119f186cee3a3854e040fcf9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 19 Nov 2013 11:48:42 +0100 Subject: [PATCH 0016/2403] add Rgputools easyconfigs Signed-off-by: Fotis Georgatos --- .../Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb | 29 ++++++++++++++++++ .../Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb create mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb new file mode 100644 index 0000000000..ad161b3b58 --- /dev/null +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb @@ -0,0 +1,29 @@ +name = 'Rgputools' +version = '876c10d' + +easyblock = 'RPackage' + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +git_commit_id = version +sources = ['%s.tar.gz' % git_commit_id] +source_urls = ['https://github.com/nullsatz/gputools/archive'] + +r = 'R' +rver = '3.0.2' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [('CUDA', '5.5.22', '', True)] + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +#options = {'modulename': name} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb new file mode 100644 index 0000000000..12159b9a1a --- /dev/null +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb @@ -0,0 +1,30 @@ +name = 'Rgputools' +version = "e5cb024" + +easyblock = 'RPackage' + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +git_commit_id = version +sources = ['%s.tar.gz' % git_commit_id] +source_urls = ['https://github.com/nullsatz/gputools/archive'] + +r = 'R' +rver = '3.0.2' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [('CUDA', '5.0.35', '-1', True)] +#premakeopts = 'R_HOME=/opt/apps/HPCBIOS.20130902/software/R/3.0.2-ictce-5.3.0-bare/lib64/R ' + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +options = {'modulename': name} + +moduleclass = 'tools' -- GitLab From 2f660dfab2b271f3405caae4dbfc577e774915fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2013 18:54:08 +0100 Subject: [PATCH 0017/2403] add easyconfigs for Mono, MyMediaLite and IronPython --- .../IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb | 17 +++++++++++ .../m/Mono/Mono-2.10.6-ictce-4.1.13.eb | 30 +++++++++++++++++++ .../MyMediaLite-3.10-ictce-4.1.13.eb | 14 +++++++++ 3 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb create mode 100644 easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb new file mode 100644 index 0000000000..fb3ff7bded --- /dev/null +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb @@ -0,0 +1,17 @@ +name = 'IronPython' +version = '2.7-0' +versionsuffix = '-g4fb2552' + +homepage = 'http://ironpython.net/' +description = """IronPython is an open-source implementation of the Python programming language + which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and +Python libraries, and other .NET languages can use Python code just as easily.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +# download via https://github.com/IronLanguages/main/releases +sources = ['IronLanguages-main-ipy-%(version)s%(versionsuffix)s.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb new file mode 100644 index 0000000000..05e81f5396 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb @@ -0,0 +1,30 @@ +name = 'Mono' +version = '2.10.6' + +homepage = 'http://mono-framework.com' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +# Mono required Mono to build, so there are a couple of options: +# 1) provide Mono RPMs in sources, the Mono easyblock will use them to make a tmp Mono install +# 2) assume a Mono version is available system-wide (assert using e.g. "osdependencies = ['mono-core']") +# 3) specify an already available Mono module as build dep, e.g. "builddependencies = [('Mono', '2.10.6')] + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [ + SOURCELOWER_TAR_BZ2, + # Mono requires Mono to build, so provide RPMs so Mono can be bootstrapped + 'libgdiplus-2.4.2-2.el5.kb.x86_64.rpm', + 'mono-core-2.4.2.3-2.el5.kb.x86_64.rpm', +] + +builddependencies = [ + ('Bison', '2.6.5'), + ('gettext', '0.18.2'), +] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb new file mode 100644 index 0000000000..21917e5c28 --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.10' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://www.mymedialite.net/download/'] +sources = ['%(name)s-%(version)s.src.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lib' -- GitLab From 98193c5ea05da3a6bf96e527a5852fa9d3aff7f7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 30 Dec 2013 03:28:39 +0100 Subject: [PATCH 0018/2403] make upstream version explicit in namespace Signed-off-by: Fotis Georgatos --- ...0.2.eb => Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb} | 6 +++--- ...0.2.eb => Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb} | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/r/Rgputools/{Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb => Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb} (88%) rename easybuild/easyconfigs/r/Rgputools/{Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb => Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb} (89%) diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb similarity index 88% rename from easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb rename to easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb index ad161b3b58..50a7c3c196 100644 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-876c10d-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb @@ -1,5 +1,6 @@ name = 'Rgputools' -version = '876c10d' +version = '0.28' +versionsuffix = '-876c10d' easyblock = 'RPackage' @@ -9,8 +10,7 @@ description = """This package provides R interfaces to a handful of common funct toolchain = {'name': 'ictce', 'version': '5.3.0'} -git_commit_id = version -sources = ['%s.tar.gz' % git_commit_id] +sources = ['%s.tar.gz' % versionsuffix[1:]] source_urls = ['https://github.com/nullsatz/gputools/archive'] r = 'R' diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb similarity index 89% rename from easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb rename to easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb index 12159b9a1a..603ade0f36 100644 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-e5cb024-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-e5cb024-ictce-5.3.0-R-3.0.2.eb @@ -1,5 +1,6 @@ name = 'Rgputools' -version = "e5cb024" +version = '0.28' +versionsuffix = '-e5cb024' easyblock = 'RPackage' @@ -9,8 +10,7 @@ description = """This package provides R interfaces to a handful of common funct toolchain = {'name': 'ictce', 'version': '5.3.0'} -git_commit_id = version -sources = ['%s.tar.gz' % git_commit_id] +sources = ['%s.tar.gz' % versionsuffix[1:]] source_urls = ['https://github.com/nullsatz/gputools/archive'] r = 'R' -- GitLab From 7747ded2dc5df670a0bdf5108fa5bd848d243f3a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 10 Jan 2014 03:21:15 +0100 Subject: [PATCH 0019/2403] remove rgputools/876c10d Signed-off-by: Fotis Georgatos --- ...utools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb diff --git a/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb deleted file mode 100644 index 50a7c3c196..0000000000 --- a/easybuild/easyconfigs/r/Rgputools/Rgputools-0.28-876c10d-ictce-5.3.0-R-3.0.2.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'Rgputools' -version = '0.28' -versionsuffix = '-876c10d' - -easyblock = 'RPackage' - -homepage = 'https://github.com/nullsatz/gputools/wiki' -description = """This package provides R interfaces to a handful of common functions implemented - using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -sources = ['%s.tar.gz' % versionsuffix[1:]] -source_urls = ['https://github.com/nullsatz/gputools/archive'] - -r = 'R' -rver = '3.0.2' -versionsuffix = '-%s-%s' % (r, rver) - -dependencies = [('CUDA', '5.5.22', '', True)] - -sanity_check_paths = { - 'files': ["gputools/libs/gputools.so"], - 'dirs': [] -} - -#options = {'modulename': name} - -moduleclass = 'tools' -- GitLab From 1053847fd144db8ad893982d3cc4f564360ceafe Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 4 Feb 2014 18:07:02 +0100 Subject: [PATCH 0020/2403] CONTRAlign-2.01 goolf-1.4.10 --- .../CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../CONTRAlign-2.01-rna-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../c/CONTRAlign/contralign-gcc47.patch | 21 +++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb new file mode 100644 index 0000000000..6255d5289d --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAlign' +version = '2.01-proteins' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contralign/' +description = ''' CONditional TRAining for Protein Sequence Alignment ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-proteins'))] + +patches = ['contralign-gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for protein input. Check docs for details +makeopts = 'MODEL_TYPE="-DRNA=0"' + +files_to_copy = [(['contralign', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb new file mode 100644 index 0000000000..50d30ad789 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAlign' +version = '2.01-rna' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contralign/' +description = ''' CONditional TRAining for Protein Sequence Alignment ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-rna'))] + +patches = ['contralign-gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for RNA input. Check docs for details +makeopts = 'MODEL_TYPE="-DRNA=1"' + +files_to_copy = [(['contralign', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch new file mode 100644 index 0000000000..02e1a2bc34 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch @@ -0,0 +1,21 @@ +--- contralign.orig/src/Makefile 2008-08-15 03:06:30.000000000 +0200 ++++ contralign/src/Makefile 2014-02-04 17:25:31.364788280 +0100 +@@ -23,7 +23,7 @@ + -ffast-math -funroll-all-loops -funsafe-math-optimizations \ + -fpeel-loops -Winline --param large-function-growth=100000 \ + --param max-inline-insns-single=100000 \ +- --param inline-unit-growth=100000 ++ --param inline-unit-growth=100000 -fpermissive + + OTHER_FLAGS = + +--- contralign.orig/src/Utilities.cpp 2008-08-14 02:08:30.000000000 +0200 ++++ contralign/src/Utilities.cpp 2014-02-04 17:25:05.483971266 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; -- GitLab From 199c7e07987d6d591806acbea4faafee80de0222 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Feb 2014 15:00:39 +0100 Subject: [PATCH 0021/2403] Raster3D-3.0-2-goolf-1.4.10.eb --- .../r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb new file mode 100644 index 0000000000..1b41f400d7 --- /dev/null +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'Raster3D' +version = '3.0-2' + +homepage = 'http://skuld.bmsc.washington.edu/raster3d/' +description = """ Raster3D is a set of tools for generating high quality raster images + of proteins or other molecules. The core program renders spheres, triangles, cylinders, + and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an + efficient software Z-buffer algorithm which is independent of any graphics hardware. + Ancillary programs process atomic coordinates from PDB files into rendering descriptions for + pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also + be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, + shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%(name)s_%(version)s.tar.gz'] + +skipsteps = ['configure'] +makeopts = ' linux && make all' +installopts = 'prefix=%(installdir)s' + +# this are RHEL/CentOS package names +osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] + +modextrapaths = {'R3D_LIB': 'share/Raster3D/materials'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["avs2ps", "balls", "normal3d", "rastep", "render", + "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e2cd85d6891a38543e1779d24f26b5f2f195a6d2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Feb 2014 19:52:46 +0100 Subject: [PATCH 0022/2403] added EB style dependencies and required eb files --- .../libjpeg-turbo-1.3.0-goolf-1.4.10.eb | 21 +++++++++++++++++++ .../r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 11 ++++++++-- 2 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..e33c2344b7 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +name = 'libjpeg-turbo' +version = '1.3.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.07'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb index 1b41f400d7..c787473f52 100644 --- a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -25,14 +25,21 @@ skipsteps = ['configure'] makeopts = ' linux && make all' installopts = 'prefix=%(installdir)s' +dependencies = [ + ('libjpeg-turbo', '1.3.0'), + ('libpng', '1.6.2'), + ('LibTIFF', '4.0.3'), +] + # this are RHEL/CentOS package names -osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] +# in case you prefer to rely in OS dependencies +#osdependencies = [('libjpeg-turbo-devel', 'libpng-devel', 'libtiff-devel')] modextrapaths = {'R3D_LIB': 'share/Raster3D/materials'} sanity_check_paths = { 'files': ['bin/%s' % x for x in ["avs2ps", "balls", "normal3d", "rastep", "render", - "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], + "ribbon", "rings3d", "rods", "stereo3d", "worms" ]], 'dirs': [] } -- GitLab From d041060bb0ad8ab463dae87f32ed688975bb2f01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Mar 2014 19:55:57 +0100 Subject: [PATCH 0023/2403] add easyconfigs for HEALPix and CRPropa + deps --- .../c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb | 20 ++++++++++ .../c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb | 25 ++++++++++++ .../c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb | 37 ++++++++++++++++++ .../c/CRPropa/CRPropa_no-docs.patch | 11 ++++++ .../d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb | 18 +++++++++ .../h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb | 15 +++++++ .../libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 27 +++++++++++++ .../r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 39 +++++++++++++++++++ .../r/ROOT/ROOT-v5_recent-ifort.patch | 11 ++++++ 9 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb new file mode 100644 index 0000000000..3653e27ca4 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'CFITSIO' +version = '3.350' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files':["lib/libcfitsio.a"], + 'dirs':["include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..09d2be584e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s.tgz'] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '2.8.12')] + +# CLHEP compiles with icc instead of icpc, required out-of-source dir +srcdir = "../CLHEP" +preconfigopts = 'cd .. && mkdir obj && cd obj && export CXX="$CC" && ' +premakeopts = 'cd ../obj &&' +preinstallopts = 'cd ../obj &&' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..627472338f --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb @@ -0,0 +1,37 @@ +name = 'CRPropa' +version = '2.0.3' + +homepage = 'https://crpropa.desy.de' +description = """CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron + on their voyage through an extra galactic environment.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +# download from https://github.com/CRPropa/CRPropa2 +sources = ['%(name)s%(version_major)s-%(version)s.tar.gz'] + +patches = ['CRPropa_no-docs.patch'] + +dependencies = [ + ('CLHEP', '2.1.3.1'), + ('CFITSIO', '3.350'), + ('ROOT', 'v5.34.13'), + ('FFTW', '3.3.3'), +] +builddependencies = [('Doxygen', '1.8.5')] + +configopts = '--with-clhep-path=$EBROOTCLHEP/bin' +configopts += '--with-cfitsio-include=$EBROOTCFITSIO/include --with-cfitsio-library=$EBROOTCFITSIO/lib ' +configopts += '--with-root=$EBROOTROOT/lib' + +# download and install the photo disintegration data package +premakeopts = './GetPDCrossSections.sh && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/CRPropa"], + 'dirs': ["lib", "share"], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch b/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch new file mode 100644 index 0000000000..f422512b07 --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch @@ -0,0 +1,11 @@ +--- Makefile.in.orig 2014-03-26 17:18:53.474997093 +0100 ++++ Makefile.in 2014-03-26 17:19:18.844596386 +0100 +@@ -291,7 +291,7 @@ + AM_CPPFLAGS = $(GNL_CPPFLAGS) + + #SUBDIRS = External doc sophia dint src +-SUBDIRS = External sophia sibyll dint src doc ++SUBDIRS = External sophia sibyll dint src # doc + EXTRA_DIST = sophia/src/sophia.h sibyll/sibyll.h src/Interactions/proton_f77 src/Interactions/proton_sophia dint/src/tables sysdep.h get_externals.sh GetPDCrossSections.sh HalfLifeTable doc/Doxyfile COPYRIGHT doc/UserGuide.tex doc/precision_traj.ps doc/PhotonDensityCollection2.eps doc/crpdetector.eps doc/AllIRBzEvolutionModelsCan.eps IRBzRedshiftEvol_Kneiske examples/GettingStarted Plot + all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..e87a654b01 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.5' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, +IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '3.0.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb new file mode 100644 index 0000000000..597c5e6d42 --- /dev/null +++ b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb @@ -0,0 +1,15 @@ +name = 'HEALPix' +version = '2.20a' + +homepage = 'http://healpix.sourceforge.net/' +description = """Hierarchical Equal Area isoLatitude Pixelation of a sphere.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['Healpix_%(version)s_2011Feb09.tar.gz'] + +dependencies = [('CFITSIO', '3.350')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..ef442f4bb5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.7'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb new file mode 100644 index 0000000000..e025c77b02 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +name = 'ROOT' +version = 'v5.34.13' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', +] + +python = 'Python' +pyver = '2.7.6' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch b/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch new file mode 100644 index 0000000000..ad687ba67c --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch @@ -0,0 +1,11 @@ +--- root/config/Makefile.linuxx8664icc.orig 2013-12-02 17:22:25.630583702 +0100 ++++ root/config/Makefile.linuxx8664icc 2013-12-02 17:22:51.951053273 +0100 +@@ -87,7 +87,7 @@ + F77 = ifort + F77FLAGS = -fPIC + ifeq ($(findstring $(ICC_MAJOR),11 10 9),) +-F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib|') \ ++F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib/intel64|') \ + -lifcore + F77FLAGS += -m64 + else -- GitLab From e263dd04591bc6046ad0bfd26493629d45534215 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Mar 2014 20:34:25 +0100 Subject: [PATCH 0024/2403] add missing Bison easyconfig file --- .../b/Bison/Bison-3.0.1-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb new file mode 100755 index 0000000000..1c5fae9cf7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '3.0.1' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs':[], +} + +moduleclass = 'lang' -- GitLab From fd7ee5a2dce9f9f70a88a109e44b3fabb5e1293f Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 20:45:56 +0100 Subject: [PATCH 0025/2403] BEDOPS-2.4.1-GCC-4.8.2.eb --- .../b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..f97abdf878 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = "BEDOPS" +version = "2.4.1" + +homepage = 'https://github.com/bedops/bedops' +description = """ BEDOPS is an open-source command-line toolkit that performs highly + efficient and scalable Boolean and other set operations, statistical calculations, + archiving, conversion and other management of genomic data of arbitrary scale.""" + +# this application requires GCC-4.8.x or higher +# be aware if you switch to a different toolchain +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +source_urls = ['https://github.com/bedops/bedops/archive/'] +sources = ['v%(version)s.tar.gz'] + +makeopts = ' static && make install' + +parallel = 1 + +files_to_copy = ["bin"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From cf4b6fd52dd38274d226e5bc84bbd2003102af15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 May 2014 13:47:04 +0200 Subject: [PATCH 0026/2403] add ictce easyconfig file for VCFtools --- .../p/Perl/Perl-5.16.3-ictce-5.5.0.eb | 225 ++++++++++++++++++ ...VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb | 39 +++ 2 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..106bbda74e --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb @@ -0,0 +1,225 @@ +name = 'Perl' +version = '5.16.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['exitcode_error.patch'] + +runtest = 'test' + +exts_list = [ + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/GAAS/'], + }), + ('Data::Stag', '0.11', { + 'source_tmpl': 'Data-Stag-0.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/CMUNGALL/'], + }), + ('DB_File', '1.827', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + }), + ('DBI', '1.625', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + }), + ('Bio::Perl', '1.6.901', { + 'source_tmpl': 'BioPerl-1.6.901.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + 'patches': ['BioPerl_disable-broken-test.patch'], + }), + ('Sub::Uplevel', '0.24', { + 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + }), + ('Tree::DAG_Node', '1.11', { + 'source_tmpl': 'Tree-DAG_Node-1.11.tgz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + }), + ('Try::Tiny', '0.12', { + 'source_tmpl': 'Try-Tiny-0.12.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Test::Fatal', '0.010', { + 'source_tmpl': 'Test-Fatal-0.010.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + }), + ('Test::Exception', '0.31', { + 'source_tmpl': 'Test-Exception-0.31.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/ADIE/'], + }), + ('Test::Warn', '0.24', { + 'source_tmpl': 'Test-Warn-0.24.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/CHORNY/'], + }), + ('Test::Requires', '0.06', { + 'source_tmpl': 'Test-Requires-0.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + }), + ('Test::Tester', '0.108', { + 'source_tmpl': 'Test-Tester-0.108.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/ADAMK/'], + }), + ('Sub::Install', '0.926', { + 'source_tmpl': 'Sub-Install-0.926.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Data::OptList', '0.107', { + 'source_tmpl': 'Data-OptList-0.107.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/RJBS/'], + }), + ('Sub::Exporter', '0.985', { + 'source_tmpl': 'Sub-Exporter-0.985.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Test::Output', '1.01', { + 'source_tmpl': 'Test-Output-1.01.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/BDFOY/'], + }), + ('Module::Runtime', '0.013', { + 'source_tmpl': 'Module-Runtime-0.013.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/ZEFRAM/'], + }), + ('Module::Implementation', '0.06', { + 'source_tmpl': 'Module-Implementation-0.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + }), + ('List::MoreUtils', '0.33', { + 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/List/ADAMK/'], + }), + ('Package::DeprecationManager', '0.13', { + 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.02', { + 'source_tmpl': 'Dist-CheckConflicts-0.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Dist/DOY/'], + }), + ('Package::Stash', '0.34', { + 'source_tmpl': 'Package-Stash-0.34.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + }), + ('Class::Load', '0.20', { + 'source_tmpl': 'Class-Load-0.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Class/DROLSKY/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FLORA/'], + }), + ('Eval::Closure', '0.08', { + 'source_tmpl': 'Eval-Closure-0.08.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001010', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001010.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FREW/'], + }), + ('Devel::GlobalDestruction', '0.11', { + 'source_tmpl': 'Devel-GlobalDestruction-0.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Devel/'], + }), + ('boolean', '0.30', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tie/CHORNY/'], + }), + ('Moose', '2.0801', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + }), + ('Params::Validate', '1.07', { + 'source_tmpl': 'Params-Validate-1.07.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + }), + ('DateTime::Locale', '0.45', { + 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Class/ABW/'], + }), + ('DateTime::TimeZone', '1.58', { + 'source_tmpl': 'DateTime-TimeZone-1.58.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('DateTime', '1.01', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/DWHEELER/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/File/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + }), + ('IO::HTML', '1.00', { + 'source_tmpl': 'IO-HTML-1.00.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/LWP/GAAS/'], + }), + ('URI', '1.60', { + 'source_urls': ['http://www.cpan.org/modules/by-module/URI/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/PETDANCE/'], + }), + ('HTML::Entities', '3.70', { + 'source_tmpl': 'HTML-Parser-3.70.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/GAAS/'], + }), + ('AnyEvent', '7.04', { + 'source_urls': ['http://www.cpan.org/modules/by-module/AnyEvent/MLEHMANN/'], + }), + ('Mouse', '1.05', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MouseX/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..1350a7b674 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'VCFtools' +version = '0.1.11' + +easyblock = 'MakeCp' + +homepage = "http://vcftools.sourceforge.net/" +description = """The aim of VCFtools is to provide + methods for working with VCF files: validating, + merging, comparing and calculate some basic population + genetic statistics. """ + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin", "lib"] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 06fd2565050f6769fb6d2ca83b245bf04d63f8a3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 7 May 2014 11:55:19 +0200 Subject: [PATCH 0027/2403] mrFAST and mrsFAST easyconfigs for goolf and ictce toolchains --- .../m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 33 ++++++++++++ .../m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 35 +++++++++++++ .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 33 ++++++++++++ .../m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 35 +++++++++++++ .../mrsFAST-2.6.0.4-intel-compiler.patch | 17 ++++++ .../mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb | 35 +++++++++++++ .../mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb | 37 +++++++++++++ .../mrsFAST-Ultra-3.3.1-intel-compiler.patch | 52 +++++++++++++++++++ 8 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..a66b9f116e --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +files_to_copy = [ + (['mrfast'], 'bin'), + "TODO", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrfast", "TODO", "LICENSE"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..a045864ca0 --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +makeopts = ' CC=$CC' + +files_to_copy = [ + (['mrfast'], 'bin'), + "TODO", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrfast", "TODO", "LICENSE"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..994e7e7c7f --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +parallel = 1 + +files_to_copy = [ + (['mrsfast'], 'bin'), + "Changelog", +] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb new file mode 100644 index 0000000000..acbe7af340 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['mrsFAST-2.6.0.4-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ + (['mrsfast'], 'bin'), + "Changelog", +] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch new file mode 100644 index 0000000000..085ff27bd8 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch @@ -0,0 +1,17 @@ +diff -ru mrsfast-2.6.0.4.orig/Makefile mrsfast-2.6.0.4/Makefile +--- mrsfast-2.6.0.4.orig/Makefile 2013-07-24 00:53:41.000000000 +0200 ++++ mrsfast-2.6.0.4/Makefile 2014-05-07 11:35:36.394689000 +0200 +@@ -1,3 +1,5 @@ ++CC=icc ++ + ALL: mrsfast + + LDFLAGS=-s -static +@@ -5,5 +7,5 @@ + CFLAGS= -O2 -s + + mrsfast: baseFAST.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o +- gcc $^ -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) $^ -o $@ ${LDFLAGS} ${LIBS} + rm *.o +Only in mrsfast-2.6.0.4: mrsfast diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7f663058f9 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST-Ultra' +version = '3.3.1' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/mrsfast/files/', 'download')] +sources = [SOURCELOWER_ZIP] + +parallel = 1 + +files_to_copy = [ + (['mrsfast', 'snp_indexer'], 'bin'), + "HELP", + "Changelog", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrsfast", "bin/snp_indexer"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..70a21c5c28 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mrsFAST-Ultra' +version = '3.3.1' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [('http://sourceforge.net/projects/mrsfast/files/', 'download')] +sources = [SOURCELOWER_ZIP] + +patches = ['mrsFAST-Ultra-3.3.1-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ + (['mrsfast', 'snp_indexer'], 'bin'), + "HELP", + "Changelog", + "LICENSE" +] + +sanity_check_paths = { + 'files': ["bin/mrsfast", "bin/snp_indexer"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch new file mode 100644 index 0000000000..2c61c608c2 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-intel-compiler.patch @@ -0,0 +1,52 @@ +diff -ru mrsfast-ultra-3.3.1.orig/Makefile mrsfast-ultra-3.3.1/Makefile +--- mrsfast-ultra-3.3.1.orig/Makefile 2014-03-31 10:36:25.000000000 +0200 ++++ mrsfast-ultra-3.3.1/Makefile 2014-05-07 11:44:59.677675000 +0200 +@@ -1,3 +1,4 @@ ++CC=icc + DEBUG := 0 + PROFILE := 0 + MRSFAST_VERSION := "3.3.1" +@@ -18,13 +19,13 @@ + + mrsfast: + ifeq ($(shell uname -s),Linux) +- gcc -w $(objects) -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) -w $(objects) -o $@ ${LDFLAGS} ${LIBS} + else +- gcc -Wl,-no_pie -fno-pic -w $(objects) -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) -Wl,-no_pie -fno-pic -w $(objects) -o $@ ${LDFLAGS} ${LIBS} + endif + + snp_indexer: SNPIndexer.o +- gcc $^ -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) $^ -o $@ ${LDFLAGS} ${LIBS} + + clean: + @rm -f $(objects) +@@ -41,7 +42,7 @@ + @ld -r -b binary -o HELP.o HELP + else + @touch HELPstub.c +- gcc -o HELPstub.o -c HELPstub.c ++ $(CC) -o HELPstub.o -c HELPstub.c + ld -r -o HELP.o -sectcreate binary HELP HELP HELPstub.o + endif + +@@ -62,7 +63,7 @@ + $(shell echo "-DSSE4=0") + else + $(eval CFLAGS = $(CFLAGS) \ +- $(shell gv=`gcc -dumpversion`; \ ++ $(shell gv=`$(CC) -dumpversion`; \ + sc=`grep -c "sse4" /proc/cpuinfo`; \ + echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}')) + endif +@@ -71,7 +72,7 @@ + $(shell echo "-DSSE4=0") + else + $(eval CFLAGS = $(CFLAGS) \ +- $(shell gv=`gcc -dumpversion`; \ ++ $(shell gv=`$(CC) -dumpversion`; \ + sc=`sysctl -n machdep.cpu.features | grep -c "SSE4"` ;\ + echo $$sc.$$gv | awk -F. '{if($$1>0 && $$2>=4 && $$3>=4) print "-DSSE4=1 -msse4.2"; else print "-DSSE4=0"}')) + endif -- GitLab From 5fc261e843dda742a0e3554e18237cce85c1ddf1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 7 May 2014 14:31:33 +0200 Subject: [PATCH 0028/2403] drFAST easyconfigs for goolf and ictce toolchains --- .../d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 32 +++++++++++++++++ .../d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 34 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..571b8bd17f --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +parallel = 1 + +files_to_copy = [ + (['drfast'], 'bin'), + "README.txt" +] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb new file mode 100644 index 0000000000..6036f2cf05 --- /dev/null +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'drFAST' +version = '1.0.0.0' + +homepage = 'http://drfast.sourceforge.net/' +description = """ drFAST is designed to map di-base reads (SOLiD color space reads) + to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_ZIP] + +parallel = 1 + +makeopts = ' CC=$CC' + +files_to_copy = [ + (['drfast'], 'bin'), + "README.txt" +] + +sanity_check_paths = { + 'files': ["bin/drfast", "README.txt"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From 798b23874b34465652569391971949979fe545fd Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 20 May 2014 19:45:00 +0200 Subject: [PATCH 0029/2403] MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb --- .../MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb new file mode 100644 index 0000000000..04b13ba339 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +versionsuffix = '_2014-04-25' + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +# first six digits of the commit id we will download from github +git_commit_id = '24cf06' +sources = ['%s.tar.gz' % (git_commit_id)] + +parallel = 1 + +start_dir = "src" + +makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [""], +} + +moduleclass = 'bio' + -- GitLab From 1f32bf41c0ae03bf32a9b2eec17c52bf8677b2f4 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 3 Jun 2014 23:25:22 +0200 Subject: [PATCH 0030/2403] added makeopts to both easyconfigs --- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 571b8bd17f..69bc7179e6 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +makeopts = ' CC="$CC"' + parallel = 1 files_to_copy = [ diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 6036f2cf05..e6d4edb800 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -17,9 +17,9 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] -parallel = 1 +makeopts = ' CC="$CC"' -makeopts = ' CC=$CC' +parallel = 1 files_to_copy = [ (['drfast'], 'bin'), -- GitLab From 7919d401a3865e2f35b7f9c81fec98447ea5cb62 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 15:27:12 +0200 Subject: [PATCH 0031/2403] added missing zlib dependency --- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 69bc7179e6..0e1f21cdae 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +dependencies = [('zlib', '1.2.8')] + makeopts = ' CC="$CC"' parallel = 1 diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index e6d4edb800..7931bee0d2 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_ZIP] +dependencies = [('zlib', '1.2.8')] + makeopts = ' CC="$CC"' parallel = 1 -- GitLab From 45b77c59fba479457a6b725e643620ff3d0bf829 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:50:52 +0200 Subject: [PATCH 0032/2403] small style fixes --- .../easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 7 ++----- .../easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 7 ++----- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 0e1f21cdae..9488117544 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,14 +23,11 @@ makeopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ - (['drfast'], 'bin'), - "README.txt" -] +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 7931bee0d2..226f9d0f9b 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -23,14 +23,11 @@ makeopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ - (['drfast'], 'bin'), - "README.txt" -] +files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From f7bfbbd0835ae7108ebf6f83fb741415bffcb1cd Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:56:59 +0200 Subject: [PATCH 0033/2403] added git_commit_id to versionsuffix --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 04b13ba339..690619ca2b 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -versionsuffix = '_2014-04-25' +versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' description = """ MOSAIK is a reference-guided aligner for next-generation -- GitLab From ae317c6a0ecf5902129a9881c1607d01f1fb0154 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Jun 2014 23:57:19 +0200 Subject: [PATCH 0034/2403] style fix in sanity_check --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 690619ca2b..5440998f01 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -30,7 +30,7 @@ files_to_copy = ["bin", "../README", "demo"] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 348e144e077fed8529b3329038720ecbb24a56ab Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:05:59 +0200 Subject: [PATCH 0035/2403] moved git_commit_id up --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 5440998f01..491953beff 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -7,6 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' @@ -16,8 +17,6 @@ description = """ MOSAIK is a reference-guided aligner for next-generation toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] -# first six digits of the commit id we will download from github -git_commit_id = '24cf06' sources = ['%s.tar.gz' % (git_commit_id)] parallel = 1 -- GitLab From ee32022c3258f592b06bbd52ee42deccb42bdf8a Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:06:51 +0200 Subject: [PATCH 0036/2403] added ictce easyconfig --- .../MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb new file mode 100644 index 0000000000..d420812af7 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +parallel = 1 + +start_dir = "src" + +makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From b7a9ad31bb2bd7a2a7049bffaf74db4c6b23a7e9 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Jun 2014 00:27:54 +0200 Subject: [PATCH 0037/2403] files_to_copy in single line. style fixes --- .../m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 8 ++------ .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 10 +++------- .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 7 ++----- .../m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 7 ++----- .../m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb | 9 ++------- .../m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb | 9 ++------- 6 files changed, 13 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index a66b9f116e..83547d99c7 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -19,15 +19,11 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -files_to_copy = [ - (['mrfast'], 'bin'), - "TODO", - "LICENSE" -] +files_to_copy = [ (['mrfast'], 'bin'), "TODO", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrfast", "TODO", "LICENSE"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index a045864ca0..a2eafd5a27 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -19,17 +19,13 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -makeopts = ' CC=$CC' +makeopts = ' CC="$CC"' -files_to_copy = [ - (['mrfast'], 'bin'), - "TODO", - "LICENSE" -] +files_to_copy = [ (['mrfast'], 'bin'), "TODO", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrfast", "TODO", "LICENSE"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index 994e7e7c7f..b2b767778f 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -20,14 +20,11 @@ sources = [SOURCELOWER_ZIP] parallel = 1 -files_to_copy = [ - (['mrsfast'], 'bin'), - "Changelog", -] +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] sanity_check_paths = { 'files': ["bin/mrsfast"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index acbe7af340..9b11e23227 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -22,14 +22,11 @@ patches = ['mrsFAST-2.6.0.4-intel-compiler.patch'] parallel = 1 -files_to_copy = [ - (['mrsfast'], 'bin'), - "Changelog", -] +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] sanity_check_paths = { 'files': ["bin/mrsfast"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb index 7f663058f9..a714d32adb 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-goolf-1.4.10.eb @@ -20,16 +20,11 @@ sources = [SOURCELOWER_ZIP] parallel = 1 -files_to_copy = [ - (['mrsfast', 'snp_indexer'], 'bin'), - "HELP", - "Changelog", - "LICENSE" -] +files_to_copy = [ (['mrsfast', 'snp_indexer'], 'bin'), "HELP", "Changelog", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrsfast", "bin/snp_indexer"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb index 70a21c5c28..6ed2b7907b 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-Ultra-3.3.1-ictce-6.2.5.eb @@ -22,16 +22,11 @@ patches = ['mrsFAST-Ultra-3.3.1-intel-compiler.patch'] parallel = 1 -files_to_copy = [ - (['mrsfast', 'snp_indexer'], 'bin'), - "HELP", - "Changelog", - "LICENSE" -] +files_to_copy = [ (['mrsfast', 'snp_indexer'], 'bin'), "HELP", "Changelog", "LICENSE" ] sanity_check_paths = { 'files': ["bin/mrsfast", "bin/snp_indexer"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 5eeb648a54378bec4b955d158305ca202b4dba2b Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 10 Jun 2014 17:05:31 +0200 Subject: [PATCH 0038/2403] added missing zlib dependency --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 2 ++ .../easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index 491953beff..afc62c9a6c 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -19,6 +19,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] sources = ['%s.tar.gz' % (git_commit_id)] +dependencies = [('zlib', '1.2.8')] + parallel = 1 start_dir = "src" diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb index d420812af7..47308d8d3d 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -19,6 +19,8 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] sources = ['%s.tar.gz' % (git_commit_id)] +dependencies = [('zlib', '1.2.8')] + parallel = 1 start_dir = "src" -- GitLab From 2478e8f498e3f9528db6f9f2fb58b15f8be54296 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 29 Jun 2014 13:24:50 +0200 Subject: [PATCH 0039/2403] splitRef-0.0.2.eb --- .../easyconfigs/s/splitRef/splitRef-0.0.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb new file mode 100644 index 0000000000..f997865645 --- /dev/null +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'splitRef' +version = '0.0.2' + +homepage = 'http://www.sph.umich.edu/csg/yli/splitRef/index.html' +description = """ splitRef splits a reference haplotype file into smaller files + with subsets of markers. The current version is a pre-release. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.sph.umich.edu/csg/yli/splitRef/download/'] +sources = ['%s.V%s.tgz' % (name, version.replace(".",""))] + +sanity_check_paths = { + 'files': ["splitRef_V002/splitRef.pl"], + 'dirs': ["examples"] +} + +# add folder splitRef_V002 to PATH +modextrapaths = { + 'PATH': '%s_V%s' % (name, version.replace(".","")) +} + +moduleclass = 'bio' + -- GitLab From 4137050e516053e1e78dd8c9c16d10744e04ecec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:47:42 +0200 Subject: [PATCH 0040/2403] add easyconfig for FFindex --- .../f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb new file mode 100755 index 0000000000..3218a6e11d --- /dev/null +++ b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +name = "FFindex" +version = "0.9.9" + +homepage = 'http://www.splashground.de/~andy/programs/FFindex/' +description = """simple index/database for huge amounts of small files""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.splashground.de/~andy/programs/FFindex/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +start_dir = 'src' + +makeopts = 'USEMPI=1' +installopts = "USEMPI=1 INSTALL_DIR=%(installdir)s" + +runtest = 'test' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ffindex_%s' % x for x in ['apply', 'build', 'from_fasta', 'get', 'modify', 'unpack']] + + ['lib64/libffindex.a', 'lib64/libffindex.so'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 12638f1690a6140bbd4fca39077f553d614ef6a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:49:14 +0200 Subject: [PATCH 0041/2403] add easyconfig for CFITSIO v3.300 --- .../c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb new file mode 100755 index 0000000000..06ebf30047 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'CFITSIO' +version = '3.300' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files':["lib/libcfitsio.a"], + 'dirs':["include"], +} + +moduleclass = 'lib' -- GitLab From 2e771de754ede797c44db85db7c763c7daaabfb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:54:07 +0200 Subject: [PATCH 0042/2403] add easyconfigs for log4cplus --- .../log4cplus-1.0.4.3-ictce-5.5.0.eb | 19 +++++++++++++++++++ .../log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb create mode 100755 easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb new file mode 100755 index 0000000000..e88e8c2f72 --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +name = 'log4cplus' +version = '1.0.4.3' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb new file mode 100755 index 0000000000..f5511eacf6 --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +name = 'log4cplus' +version = '1.1.2' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' -- GitLab From 0b80f86d10777c4124bb3505523540952ad8d333 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:54:54 +0200 Subject: [PATCH 0043/2403] add easyconfig for RDMC --- .../r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100755 easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb new file mode 100755 index 0000000000..b6cf4c64fb --- /dev/null +++ b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +name = 'RDMC' +version = '2.9.5' + +homepage = 'http://code.icecube.wisc.edu/' +description = "The AMANDA-era RDMC physics library" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://code.icecube.wisc.edu/tools/distfiles/%(namelower)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [('texinfo', '5.2')] + +modextrapaths = {'LD_LIBRARY_PATH': 'lib/rdmc'} + +sanity_check_paths = { + 'files': ["bin/cpfeil", "include/rdmc/rdmc.h", "include/rdmc/rdmc.inc", + "lib/rdmc/librdmc.a", "lib/rdmc/librdmc.so"], + 'dirs': [], +} + +moduleclass = 'phys' -- GitLab From 72f490ad08421b7cb0f23974841eae70d262d305 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:57:00 +0200 Subject: [PATCH 0044/2403] add missing texinfo easyconfig --- .../t/texinfo/texinfo-5.2-ictce-5.5.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100755 easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb new file mode 100755 index 0000000000..dc542d4583 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'texinfo' +version = '5.2' + +homepage = 'http://www.gnu.org/software/texinfo/' +description = "Texinfo is the official documentation format of the GNU project." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://ftpmirror.gnu.org/texinfo'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['info', 'infokey', 'install-info', 'makeinfo', 'pdftexi2dvi', 'pod2texi', + 'texi2any', 'texi2dvi', 'texi2pdf', 'texindex']], + 'dirs': ["bin", "share"], +} + +moduleclass = 'tools' -- GitLab From 6bab96d03354a5d2bed8d5920cdfa01e028a4279 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Oct 2014 12:57:32 +0200 Subject: [PATCH 0045/2403] fix srcversion for CFITSIO v3.300 --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb index 06ebf30047..e2fd327b03 100755 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -8,7 +8,7 @@ FITS (Flexible Image Transport System) data format.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -srcversion = '%s0' % version.replace('.', '') +srcversion = version.replace('.', '') source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] -- GitLab From f6cedee8d621c866e774eeb491967ba9950d2e18 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 11:12:23 +0100 Subject: [PATCH 0046/2403] khmer-1.1-goolf-1.4.10-Python-2.7.5.eb --- .../khmer-1.1-goolf-1.4.10-Python-2.7.5.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..3e1822af64 --- /dev/null +++ b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'khmer' +version = '1.1' + +homepage = 'https://github.com/ged-lab/khmer/' +description = """ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/ged-lab/khmer/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["count-median.py", "extract-long-sequences.py", "filter-abund.py", + "load-into-counting.py", "sample-reads-randomly.py"]], + 'dirs': ["lib/python%s/site-packages/khmer-%s-py%s-linux-x86_64.egg" % (pyshortver, version, pyshortver)], +} + +moduleclass = 'bio' -- GitLab From ef2c2773eb43f32bd3ea3702377e5ad46db01eee Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 10 Nov 2014 11:36:01 +1300 Subject: [PATCH 0047/2403] Use Binary easyblock --- .../i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb new file mode 100644 index 0000000000..e39a5d8ef3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'IMOD' +version = '4.7.12_RHEL6-64' + +homepage = 'http://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'openmp': True} + +source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] +sources = ['%(namelower)s_%(version)s.csh'] + +install_cmd = "tcsh %(namelower)s_%(version)s.csh" + +# -dir: Choose location of installation directory +# -skip: do not attempt to deploy resource files in /etc +# -yes: do not prompt for confirmation +installopts = "-dir %(installdir)s -skip -yes" + +# The assumption by the install script is that installdir will be something +# like /usr/local. So it prefixes the install location with a lot of specific +# directories that are surplus to requirements. +postinstallcmds = ["mv %(installdir)s/%(name)s/* %(installdir)s/."] + +sanity_check_paths = { + 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'vis' + -- GitLab From fe42be6c71aeea35500030e32b81d6e3bdd3a7eb Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 10 Nov 2014 16:29:05 +1300 Subject: [PATCH 0048/2403] Updates to IMOD installation, including module file --- .../i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 26 +++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb index e39a5d8ef3..cfe2281f3e 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -28,12 +28,34 @@ installopts = "-dir %(installdir)s -skip -yes" # The assumption by the install script is that installdir will be something # like /usr/local. So it prefixes the install location with a lot of specific # directories that are surplus to requirements. -postinstallcmds = ["mv %(installdir)s/%(name)s/* %(installdir)s/."] +postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" + ] +# "rm -r %(installdir)s/%(name)s-linux.*" sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], 'dirs': ['bin', 'lib'] } +# Assuming the system java /usr/java can be used. If not, we can +# cross that bridge. moduleclass = 'vis' - +modextravars = {'IMOD_DIR' : "$root", + 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", + 'FOR_DISABLE_STACK_TRACE' : 1, + 'IMOD_QTLIBDIR' : "$root/qtlib"} +modaliases = {'subm' : "submfg $* &"} +modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" + +#MODULES +#------- +#include_modpath_extensions:Include $MODULEPATH extensions specified by module naming scheme. (default: True) +#modaliases: Aliases to be defined in module file (default: {}) +#modextrapaths: Extra paths to be prepended in module file (default: {}) +#modextravars: Extra environment variables to be added to module file (default: {}) +#modloadmsg: Message that should be printed when generated module is loaded (default: {}) +#modtclfooter: Footer to include in generated module file (Tcl syntax) (default: ) +#moduleforceunload: Force unload of all modules when loading the extension (default: False) +#moduleloadnoconflict: Don't check for conflicts, unload other versions instead (default: False) -- GitLab From 17cab7e752d01bb744015e90fd81ac5013023294 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Nov 2014 19:23:05 +0100 Subject: [PATCH 0049/2403] add easyconfig for FragGeneScan --- .../FragGeneScan-1.9-intel-2014b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb new file mode 100644 index 0000000000..807f2d8eb8 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.19' + +homepage = 'http://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] + +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.py *.pl train example' + +files_to_copy = ['FragGeneScan', 'FGS_gff.py', 'post_process.pl', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FGS_gff.py', 'FragGeneScan', 'post_process.pl', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +moduleclass = 'bio' -- GitLab From 7d2d728ae5264cb4fa089323f558ad597235b1c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Nov 2014 20:42:57 +0100 Subject: [PATCH 0050/2403] fix FragGeneScan filename --- ...neScan-1.9-intel-2014b.eb => FragGeneScan-1.19-intel-2014b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/FragGeneScan/{FragGeneScan-1.9-intel-2014b.eb => FragGeneScan-1.19-intel-2014b.eb} (100%) diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb rename to easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb -- GitLab From 8b85e2f64d3e0a3ceed8e38ce49f973f50b7219e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Dec 2014 19:34:11 +0100 Subject: [PATCH 0051/2403] add easyconfig for ROOT v5.30.06 with goolf toolchain --- ...libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 27 ++++++++++++++ .../r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb create mode 100755 easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..d68ae2eaee --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb new file mode 100755 index 0000000000..9a78780f34 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +name = 'ROOT' +version = 'v5.30.06' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] + +python = 'Python' +pyver = '2.7.5' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664gcc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' -- GitLab From 29f76ad33050d5b831f116f64b79eb4dab79ef87 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 13:52:07 +1300 Subject: [PATCH 0052/2403] New easyconfigs for GROMOS++ and gromosXX --- .../g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ .../g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..1da3cc48d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(namelower)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..9b0643940a --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(name)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +moduleclass = 'bio' -- GitLab From 744b58f10247ff8f494f6baa568b945b1eade69b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 16:37:06 +1300 Subject: [PATCH 0053/2403] Added support for a Linux group for restricting to licensed users --- easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb index 1da3cc48d3..557a5258d6 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } +group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb index 9b0643940a..428ee43e0b 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb @@ -27,4 +27,5 @@ sanity_check_paths = { 'dirs': ['include/md++'], } +group = 'gromos' moduleclass = 'bio' -- GitLab From 109c8294d98e3818654707dbcccdc92d120fcacf Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 12 Jan 2015 17:21:21 +1300 Subject: [PATCH 0054/2403] New easyconfigs for GROMACS (in progress, may need renaming) --- .../GROMACS-3.3.3-goolf-1.6.10-hybrid.eb | 36 +++++++++++++++++++ .../GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb | 35 ++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb new file mode 100644 index 0000000000..cc57e59e97 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '3.3.3' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'goolf', 'version': '1.6.10'} +toolchainopts = {'openmp': True, 'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb new file mode 100644 index 0000000000..6a08fa65ef --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '3.3.3' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ +] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' -- GitLab From bd538b2ddcdae6590ec32ba6297f94009b130ea2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 14 Jan 2015 14:09:44 +1300 Subject: [PATCH 0055/2403] Improved version numbering and OpenMP and MPI variants of GROMOS --- .../GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} | 8 +++-- .../gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 36 +++++++++++++++++++ .../gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 36 +++++++++++++++++++ ... gromosXX-1.0.1737-goolf-1.5.14-serial.eb} | 8 +++-- 5 files changed, 120 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/GROMOS++/{GROMOS++-1.0-goolf-1.5.14.eb => GROMOS++-1.0.2211-goolf-1.5.14-serial.eb} (84%) create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb create mode 100644 easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb rename easybuild/easyconfigs/g/gromosXX/{gromosXX-1.0-goolf-1.5.14.eb => gromosXX-1.0.1737-goolf-1.5.14-serial.eb} (83%) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..f8faf80988 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'GROMOS++' +version = '1.0.2211' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", + "lib/gromosplugin.a", "lib/libgromos.a"], + 'dirs': ["include", "share/gromos++"], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb similarity index 84% rename from easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 557a5258d6..31c8c80c13 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'GROMOS++' -version = '1.0' +version = '1.0.2211' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s.tar.bz2'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", "lib/gromosplugin.a", "lib/libgromos.a"], diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb new file mode 100644 index 0000000000..1ca0239cec --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-mpi' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': True} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-mpi' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb new file mode 100644 index 0000000000..0845c8a493 --- /dev/null +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Benjamin P. Roberts +# New Zealand eScience Infrastructure +# The University of Auckland, Auckland, New Zealand + +easyblock = 'ConfigureMake' + +name = 'gromosXX' +version = '1.0.1737' +versionsuffix = '-openmp' + +homepage = 'http://www.gromos.net/' +description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation +computer program package, which has been developed since 1978 for the dynamic +modelling of (bio)molecules, until 1990 at the University of Groningen, The +Netherlands, and since then at the ETH, the Swiss Federal Institute of +Technology, in Zürich, Switzerland. """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True, 'usempi': False} + +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [('GSL', '1.16')] + +preconfigopts = './Config.sh &&' +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], + #'files': ["bin/md", "bin/md_mpi"], + 'dirs': ['include/md++'], +} + +group = 'gromos' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb similarity index 83% rename from easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index 428ee43e0b..d48f6a0b1f 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -6,7 +6,8 @@ easyblock = 'ConfigureMake' name = 'gromosXX' -version = '1.0' +version = '1.0.1737' +versionsuffix = '-serial' homepage = 'http://www.gromos.net/' description = """ GROMOS™ is an acronym of the GROningen MOlecular Simulation @@ -16,11 +17,14 @@ Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(name)s.tar.bz2'] +sources = ['%(name)s-%(version)s.tar.bz2'] dependencies = [('GSL', '1.16')] +preconfigopts = './Config.sh &&' + sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], #'files': ["bin/md", "bin/md_mpi"], -- GitLab From 750e44a9c09fafb64469a8e5a02000ded699cf85 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jan 2015 14:09:58 +1300 Subject: [PATCH 0056/2403] Updates as per comments --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 4 ++-- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 4 ++-- .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index f8faf80988..b0cbb9b351 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -28,7 +28,7 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 31c8c80c13..9d4e1b8c63 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -19,7 +19,7 @@ Technology, in Zürich, Switzerland. """ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': False, 'usempi': False} -sources = ['%(namelower)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GSL', '1.16')] @@ -27,7 +27,7 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/pdb2g96", "bin/gromacs2gromos", "bin/structure_factor", - "lib/gromosplugin.a", "lib/libgromos.a"], + "lib/gromosplugin.a", "lib/libgromos.a"], 'dirs': ["include", "share/gromos++"], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 1ca0239cec..323c0f50ec 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -28,7 +28,6 @@ configopts = '--enable-mpi' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index 0845c8a493..b47b02b824 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -28,7 +28,6 @@ configopts = '--enable-openmp' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d48f6a0b1f..d0b7ca517a 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -27,7 +27,6 @@ preconfigopts = './Config.sh &&' sanity_check_paths = { 'files': ["bin/md", "bin/md_mpi", "lib/libmdpp.a"], - #'files': ["bin/md", "bin/md_mpi"], 'dirs': ['include/md++'], } -- GitLab From 0f4d7484b84e888d4fd319d6fbf39bcd07a653e1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 28 Jan 2015 10:21:21 +0100 Subject: [PATCH 0057/2403] mview easyconfigs added --- .../MView-1.49-goolf-1.4.10-Perl-5.16.3.eb | 30 ++++++++++++++++++ .../MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 31 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..1d8d750921 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'MView' +version = '1.49' +versionsuffix = '-Perl-5.16.3' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextravars = { + 'PERL5LIB': '$root/lib' + } + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..f5fb2d82e3 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'MView' +version = "1.57" +versionsuffix = '-Perl-5.16.3' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextravars = { + 'PERL5LIB': '$root/lib' + } + +moduleclass = 'bio' + -- GitLab From 7c4969f9e8a9a13dc6ab37cfca17d734de6024bb Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 28 Jan 2015 10:39:21 +0100 Subject: [PATCH 0058/2403] added missing Perl deps --- .../easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb | 2 ++ .../easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb index 1d8d750921..3e83426be9 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.49-goolf-1.4.10-Perl-5.16.3.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('Perl', '5.16.3')] + sanity_check_paths = { 'files': ["bin/mview"], 'dirs': ["lib"], diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index f5fb2d82e3..0d93edc825 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('Perl', '5.16.3')] + sanity_check_paths = { 'files': ["bin/mview"], 'dirs': ["lib"], -- GitLab From 873923b04ca2661d61be0993d2088332e2757f9f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 29 Jan 2015 10:51:00 +1300 Subject: [PATCH 0059/2403] Removed group directive per request from user @boegel --- .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb | 1 - .../g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb | 1 - .../easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb | 1 - .../g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index b0cbb9b351..cd7029cdae 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -32,5 +32,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 9d4e1b8c63..2b1345c99b 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ["include", "share/gromos++"], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 323c0f50ec..3020c00623 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index b47b02b824..8cae45f338 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -31,5 +31,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index d0b7ca517a..075812f642 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -30,5 +30,4 @@ sanity_check_paths = { 'dirs': ['include/md++'], } -group = 'gromos' moduleclass = 'bio' -- GitLab From 23d6cb796cd380afc7b9a6c24e5e09e41465dbd6 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Feb 2015 16:02:00 +1300 Subject: [PATCH 0060/2403] Changes to GROMACS 3.3.3 easybuild configs --- ...10-hybrid.eb => GROMACS-3.3.3-goolf-1.5.14-hybrid.eb} | 9 ++------- ...olf-1.6.10-mt.eb => GROMACS-3.3.3-goolf-1.5.14-mt.eb} | 6 +----- 2 files changed, 3 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-3.3.3-goolf-1.6.10-hybrid.eb => GROMACS-3.3.3-goolf-1.5.14-hybrid.eb} (86%) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-3.3.3-goolf-1.6.10-mt.eb => GROMACS-3.3.3-goolf-1.5.14-mt.eb} (93%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb similarity index 86% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb index cc57e59e97..1c38a4f9de 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb @@ -18,7 +18,7 @@ homepage = 'http://www.gromacs.org' description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" -toolchain = {'name': 'goolf', 'version': '1.6.10'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True, 'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz @@ -26,11 +26,6 @@ source_urls = [ 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources 'http://gerrit.gromacs.org/download/', # regression tests sources ] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '2.8.12')] +sources = [SOURCELOWER_TAR_GZ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb similarity index 93% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb index 6a08fa65ef..ef2e2a2811 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.6.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb @@ -26,10 +26,6 @@ source_urls = [ 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources 'http://gerrit.gromacs.org/download/', # regression tests sources ] -sources = [ - SOURCELOWER_TAR_GZ -] - -builddependencies = [('CMake', '2.8.12')] +sources = [SOURCELOWER_TAR_GZ] moduleclass = 'bio' -- GitLab From 2eb06e3164fa6ed4e52210076881a16e98482523 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 3 Feb 2015 13:37:58 +1300 Subject: [PATCH 0061/2403] Multiple configopts for multiple successive builds --- .../easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb index 1c38a4f9de..3a0492ebb1 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb @@ -28,4 +28,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] +configopts = [ "", "--enable-mpi --program-suffix='mpi'" ] + moduleclass = 'bio' -- GitLab From 020fe80f5034e5af678bfa304b816042eaa4e937 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:09:23 +0100 Subject: [PATCH 0062/2403] Libint 2.0.5 for intel/2015a --- .../l/Libint/Libint-2.0.5-intel-2015a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb new file mode 100644 index 0000000000..3e31d41c43 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.5' + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['release-2-0-5.tar.gz'] +source_urls = ['https://github.com/evaleev/libint/archive/'] + +moduleclass = 'chem' -- GitLab From a408bf8a8b61d5ae228248d44d0509f670fdebb6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:15:04 +0100 Subject: [PATCH 0063/2403] Added autogen to libint-2.0.5 --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 3e31d41c43..c9f9fb6f34 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] +preconfigopts = './autogen.sh && ' + +builddependencies = [('Autotools', '20150119', '-GCC-4.9.2')] + moduleclass = 'chem' -- GitLab From 1f135d8d0400a645b961aeff8e289822fedd649b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:17:41 +0100 Subject: [PATCH 0064/2403] libint: correct toolchain spec for build deps --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index c9f9fb6f34..e05864fab6 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -13,6 +13,6 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] preconfigopts = './autogen.sh && ' -builddependencies = [('Autotools', '20150119', '-GCC-4.9.2')] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] moduleclass = 'chem' -- GitLab From 75da2a27442abbd52d79f049c775485c54eb881b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:19:28 +0100 Subject: [PATCH 0065/2403] libint: work around incorrect permisions --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index e05864fab6..4a2c6ac340 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] -preconfigopts = './autogen.sh && ' +preconfigopts = 'sh autogen.sh && ' builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From a51b7feb1d06b30aaabb930fa6210465f16978a3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:30:56 +0100 Subject: [PATCH 0066/2403] Added GMP-6 for intel/2015a --- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb new file mode 100644 index 0000000000..b9c870dbee --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0a' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 871d1105e8bc91d8940de02e1a77f1bbaabe395d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:31:13 +0100 Subject: [PATCH 0067/2403] Libint: use new deps --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 4a2c6ac340..b558f56bed 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] +dependencies = [ + ('GMP', '6.0.0a'), + ('Boost', '1.57.0', '-Python-2.7.9'), +] + preconfigopts = 'sh autogen.sh && ' builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From eb7feca830c49a4a1700fa19740bae0ca0e8b53e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:05:44 +0100 Subject: [PATCH 0068/2403] Libint: fix remarks --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index b558f56bed..25c976800b 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} -sources = ['release-2-0-5.tar.gz'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ @@ -16,8 +16,8 @@ dependencies = [ ('Boost', '1.57.0', '-Python-2.7.9'), ] -preconfigopts = 'sh autogen.sh && ' - builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +preconfigopts = 'sh autogen.sh && ' + moduleclass = 'chem' -- GitLab From 6da23c633530ece4f990404efa862d8e0375695b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:07:41 +0100 Subject: [PATCH 0069/2403] Libint: fix remarks part 2 --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 25c976800b..71dd5e8235 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -18,6 +18,7 @@ dependencies = [ builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +# no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' moduleclass = 'chem' -- GitLab From 908e17076fd7b1d777cac4fd7da56bfa65b8a310 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:44:33 +0100 Subject: [PATCH 0070/2403] Add versionsuffix for Libint. I don't like this, but there seems to be no solution for the moment. --- ...ntel-2015a.eb => Libint-2.0.5-intel-2015a-Python-2.7.9.eb} | 4 ++++ 1 file changed, 4 insertions(+) rename easybuild/easyconfigs/l/Libint/{Libint-2.0.5-intel-2015a.eb => Libint-2.0.5-intel-2015a-Python-2.7.9.eb} (74%) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb similarity index 74% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb rename to easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 71dd5e8235..5fecdd649f 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,9 @@ name = 'Libint' version = '2.0.5' +# I'm really really not happy about this. It shouldn't be here. But PSI needs Boost-Python, +# so this also uses Boost-Python, so we add a Python suffix. This needs a better solution. +# Just to be clear: Libint doesn't need python. +versionsuffix = '-Python-2.7.9' homepage = 'https://github.com/evaleev/libint' description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body -- GitLab From c62a6922633260960144dac36e5aa83285a8b0b6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:54:05 +0100 Subject: [PATCH 0071/2403] Libint: Use versionsuffix everywhere --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 5fecdd649f..8a3e779142 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ ('GMP', '6.0.0a'), - ('Boost', '1.57.0', '-Python-2.7.9'), + ('Boost', '1.57.0', versionsuffix), ] builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From b97c3f271b1641ccbc54e0f326fb4eae22e3b906 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 22:04:01 +0100 Subject: [PATCH 0072/2403] Libint: less dramatic comment --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 8a3e779142..7280d68ec2 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -1,8 +1,6 @@ name = 'Libint' version = '2.0.5' -# I'm really really not happy about this. It shouldn't be here. But PSI needs Boost-Python, -# so this also uses Boost-Python, so we add a Python suffix. This needs a better solution. -# Just to be clear: Libint doesn't need python. +# Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 versionsuffix = '-Python-2.7.9' homepage = 'https://github.com/evaleev/libint' -- GitLab From 125cf5c07cd12de0d8d87139fbf52f6e9e6c1162 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:02:29 +0100 Subject: [PATCH 0073/2403] Let icc be more strict with fp for GMP --- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb index b9c870dbee..83eeacce00 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -14,6 +14,7 @@ source_urls = ['http://ftp.gnu.org/gnu/gmp'] # enable C++ interface configopts = '--enable-cxx' +preconfigopts = 'CFLAGS="-O2 -xHost -ftz -fp-speculation=strict -fp-model precise" CFLAGS="$CFLAGS" ' runtest = 'check' -- GitLab From 006586a083e7fe72edd64064d1cc116e9c68243f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:11:46 +0100 Subject: [PATCH 0074/2403] GMP: use toolchainopts --- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb index 83eeacce00..70c2a1cb32 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -8,13 +8,13 @@ description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] # enable C++ interface configopts = '--enable-cxx' -preconfigopts = 'CFLAGS="-O2 -xHost -ftz -fp-speculation=strict -fp-model precise" CFLAGS="$CFLAGS" ' runtest = 'check' -- GitLab From a8e4451ca23a1d9d288226e61fdb81a6e2511997 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:25:51 +0100 Subject: [PATCH 0075/2403] Libint: parrallel to 1 --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 7280d68ec2..af61a2e991 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -23,4 +23,6 @@ builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] # no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' +parallel = 1 + moduleclass = 'chem' -- GitLab From a3d8f3e0cfa3c884202871c5c20ddc8bf2259a98 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 24 Feb 2015 16:24:06 +0100 Subject: [PATCH 0076/2403] MM-align --- .../m/MM-align/MM-align-1.0-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..94bf357f14 --- /dev/null +++ b/easybuild/easyconfigs/m/MM-align/MM-align-1.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'CmdCp' + +name = 'MM-align' +version = '1.0' # no version info provided. I decide it's 1.0 + +homepage = 'http://zhanglab.ccmb.med.umich.edu/MM-align/' +description = """ MM-align is an algorithm for structurally aligning + multiple-chain protein-protein complexes. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://zhanglab.ccmb.med.umich.edu/MM-align/'] +sources = ['MMalign.f'] + +skipsteps = ['source'] + +cmds_map = [('MMalign.f', '$F77 -static -O3 -ffast-math -lm -o MMalign %(source)s')] + +files_to_copy = [(['MMalign'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/MMalign'], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 55ddf938e84cf829d964180531c26db77fa55bb7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 4 Mar 2015 17:31:08 +1300 Subject: [PATCH 0077/2403] Ongoig work to get GROMACS 3.3.3 working --- .../easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb index 3a0492ebb1..2f8f9c1a0c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb @@ -28,6 +28,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = [ "", "--enable-mpi --program-suffix='mpi'" ] +configopts = [ "--enable-mpi --program-suffix='mpi'" ] moduleclass = 'bio' -- GitLab From 8f8307b45481eae369fe72c6dd9638f6b30a7a82 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 5 Mar 2015 15:29:36 +1300 Subject: [PATCH 0078/2403] Abolished multithreading config file for GROMACS 3.3.3, and updated MPI configuration file --- .../GROMACS-3.3.3-goolf-1.5.14-hybrid.eb | 33 ------------------- ...14-mt.eb => GROMACS-3.3.3-goolf-1.5.14.eb} | 3 +- 2 files changed, 1 insertion(+), 35 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb rename easybuild/easyconfigs/g/GROMACS/{GROMACS-3.3.3-goolf-1.5.14-mt.eb => GROMACS-3.3.3-goolf-1.5.14.eb} (93%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb deleted file mode 100644 index 2f8f9c1a0c..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-hybrid.eb +++ /dev/null @@ -1,33 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '3.3.3' -versionsuffix = '-hybrid' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'openmp': True, 'usempi': True} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = [ "--enable-mpi --program-suffix='mpi'" ] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb similarity index 93% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb index ef2e2a2811..6cbe4c8289 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb @@ -12,14 +12,13 @@ ## name = 'GROMACS' version = '3.3.3' -versionsuffix = '-mt' homepage = 'http://www.gromacs.org' description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'openmp': True, 'usempi': False} +toolchainopts = {'openmp': False, 'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz source_urls = [ -- GitLab From 28fb2ba796dbc1d136ff74f7dc9a8838e899642c Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 12:04:56 +0100 Subject: [PATCH 0079/2403] plinkseq easyconfig and deps --- .../p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb | 40 +++++++++++++++++++ .../p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb | 20 ++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb new file mode 100644 index 0000000000..4e81c0b2d3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PLINKSEQ' +version = '0.10' + +homepage = 'https://atgu.mgh.harvard.edu/plinkseq/' +description = """ PLINK/SEQ is an open-source C/C++ library for working with human + genetic variation data. The specific focus is to provide a platform for analytic tool + development for variation data from large-scale resequencing and genotyping projects, + particularly whole-exome and whole-genome studies. It is independent of (but designed + to be complementary to) the existing PLINK package. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://psychgen.u.hpc.mssm.edu/plinkseq_downloads/'] +sources = ['%(namelower)s-src-%(version)s.tgz'] + +dependencies = [ + ('protobuf', '2.5.0'), + ('zlib', '1.2.8') +] + +parallel = 1 + +binary_files = ["behead", "browser", "gcol", "mm", "mongoose", "pdas", "pseq", "smp", "tab2vcf"] + +files_to_copy = [(["build/execs/%s" % x for x in binary_files], "bin")] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binary_files], + 'dirs': [''] + } + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..76cd95e464 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://code.google.com/p/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GOOGLECODE_SOURCE] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [], +} + +moduleclass = 'devel' + -- GitLab From 3311fdb947e0d8f6377ce95b604142aea6052bb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 16:51:24 +0200 Subject: [PATCH 0080/2403] fix Paraver/wxPropertyGrid --- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 42 ------------------- .../wxPropertyGrid-1.4.15-GCC-4.7.3.eb | 2 +- 2 files changed, 1 insertion(+), 43 deletions(-) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb index d62b7707a8..801bff930d 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -21,50 +21,8 @@ dependencies = [ ('Boost', '1.53.0', '-serial'), ] -osdependencies = ['wxWidgets-ansi-devel'] - # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] -# --- BM ISSUE --- -# -# lib64/lib linking should be avoided by patching Paraver configure/Makefiles files -# configure/Makefile assumes everything always in lib/ -preconfigopts = [ - 'cd ptools_common_files; ', - 'ln -s -f %(installdir)s/ptools/lib64 %(installdir)s/ptools/lib; cd paraver-kernel; ', - 'ln -s -f %(installdir)s/lib64 %(installdir)s/lib; cd wxparaver;' -] -premakeopts = [ - 'cd ptools_common_files; ', - 'cd paraver-kernel; ', - 'cd wxparaver;' -] -preinstallopts = [ - 'cd ptools_common_files; ', - 'cd paraver-kernel; ', - 'cd wxparaver;' -] - -configopts = [ - '--prefix=%(installdir)s/ptools', - '--with-boost=${EBROOTBOOST}' - + ' --with-ptools-common-files=%(installdir)s/ptools', - '--with-boost=${EBROOTBOOST}' - + ' --with-wxpropgrid=wxcode_gtk2_propgrid-2.8' - + ' --with-paraver=%(installdir)s' -] - -keeppreviousinstall = True - -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ -sanity_check_paths = { - 'files': ["bin/wxparaver", "include/paraverconfig.h", - "lib64/paraver-kernel/libparaver-kernel.a"], - 'dirs': [] -} - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb index 859fce3a0d..b4eceecafb 100644 --- a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb @@ -15,7 +15,7 @@ description = """wxPropertyGrid is a property sheet control for wxWidgets. In ot toolchain = {'name': 'GCC', 'version': '4.7.3'} -osdependencies = ['wxWidgets-ansi-devel'] +osdependencies = [('wxGTK-devel', 'libwxgtk2.8-dev', 'wxWidgets-ansi-devel')] # http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] -- GitLab From 874893040bf5edbc636328421fffb7d308a91194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 00:38:06 +0200 Subject: [PATCH 0081/2403] Tau tweaks --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb index bda1e46477..008012a78d 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -30,9 +30,15 @@ dependencies = [ ('OTF', '1.12.4', "", (compname, compver)), ('PAPI', '5.2.0', "", (compname, compver)), ('PDT', '3.19', "", (compname, compver)), - ('Scalasca', '1.4.3'), - ('Score-P', '1.2.1'), - ('VampirTrace', '5.14.4'), + #('Scalasca', '1.4.3'), # requires enabling scalasca1 as extra backend + #('Score-P', '1.2.1'), # requires enabling scorep as extra backend + ('VampirTrace', '5.14.4'), # requires enabling vampirtrace as extra backend +] + +extra_backends = [ + #'scalasca1', # deprecated, use scorep backend instead (requires Scalasca v1.x as dependency) + #'vampirtrace', # deprecated, use scorep backend instead (requires VampirTrace as dependency) + 'scorep', # requires Score-P as dependency ] # http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz @@ -98,12 +104,10 @@ sanity_check_paths = { 'dirs': [] } -modextrapaths = { - 'PATH': machine + "/bin", - 'TAU_MF_DIR': machine + "/lib", - 'TAU_MAKEFILE': machine + "/lib/Makefile.tau-papi-mpi-pdt", -} + +# default measurement settings modextravars = { + 'TAU_MAKEFILE': '%(installdir)s/lib/Makefile.tau-papi-mpi-pdt', 'TAU_PROFILE': '1', 'TAU_TRACE': '0', 'TAU_CALLPATH': '1', -- GitLab From 0b7bf1c9d633097296df3711175f205c8ab27f27 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 14:42:24 +0200 Subject: [PATCH 0082/2403] Adding QuantumESPRESSO-5.1.2-ictce-7.3.5 --- .../QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb new file mode 100644 index 0000000000..a7bb611c44 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -0,0 +1,40 @@ +name = 'QuantumESPRESSO' +version = '5.1.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%(version)s.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'xspectra-%(version)s.tar.gz', + 'GWW-%(version)s.tar.gz', +] + +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/752/', # atomic-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/755/', # PHonon-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/756/', # pwcond-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/757/', # xspectra-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/758/', # tddfpt-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/760/', # neb-5.1.2.tar.gz +] + +buildopts = 'all plumed w90 want gipaw' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From d02e5a7fc948b62c7d2889e593046391932ecbb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Jun 2015 17:35:03 +0200 Subject: [PATCH 0083/2403] cleanup source_urls --- .../q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb index a7bb611c44..f94df6b8f2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -22,14 +22,9 @@ sources = [ ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # others 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/752/', # atomic-5.1.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/755/', # PHonon-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/756/', # pwcond-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/757/', # xspectra-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/758/', # tddfpt-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/760/', # neb-5.1.2.tar.gz ] buildopts = 'all plumed w90 want gipaw' -- GitLab From e5ebd2245ea20383165b4e0052d9eb8ce8591119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 09:51:45 +0200 Subject: [PATCH 0084/2403] improve comment on generic source URL --- .../q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb index f94df6b8f2..66a93062f3 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -22,7 +22,7 @@ sources = [ ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz and GWW*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz ] -- GitLab From ad4c0ddb3dae90b7ab08f8236c17f398cf4c511a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:02:45 +0200 Subject: [PATCH 0085/2403] use GCC GMP as intel and GMP don't get along --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index af61a2e991..91014bdb21 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,7 @@ sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ - ('GMP', '6.0.0a'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.57.0', versionsuffix), ] -- GitLab From 6e3352cf605895a127b60538ea57584635d1fd6e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 8 Jun 2015 11:29:16 +1200 Subject: [PATCH 0086/2403] Removed some unnecessary comments --- easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb index cfe2281f3e..1bf6bb89e6 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -31,7 +31,6 @@ installopts = "-dir %(installdir)s -skip -yes" postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" ] -# "rm -r %(installdir)s/%(name)s-linux.*" sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], @@ -48,14 +47,3 @@ modextravars = {'IMOD_DIR' : "$root", 'IMOD_QTLIBDIR' : "$root/qtlib"} modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" - -#MODULES -#------- -#include_modpath_extensions:Include $MODULEPATH extensions specified by module naming scheme. (default: True) -#modaliases: Aliases to be defined in module file (default: {}) -#modextrapaths: Extra paths to be prepended in module file (default: {}) -#modextravars: Extra environment variables to be added to module file (default: {}) -#modloadmsg: Message that should be printed when generated module is loaded (default: {}) -#modtclfooter: Footer to include in generated module file (Tcl syntax) (default: ) -#moduleforceunload: Force unload of all modules when loading the extension (default: False) -#moduleloadnoconflict: Don't check for conflicts, unload other versions instead (default: False) -- GitLab From e8b5561e40f275e54b631ee27d2b79603cb844bc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 8 Jun 2015 11:31:03 +1200 Subject: [PATCH 0087/2403] Renamed dash to underscore in the hope that fixes an assertion --- .../i/IMOD/{IMOD-4.7.12-RHEL6-64.eb => IMOD-4.7.12_RHEL6-64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/IMOD/{IMOD-4.7.12-RHEL6-64.eb => IMOD-4.7.12_RHEL6-64.eb} (100%) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb similarity index 100% rename from easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb rename to easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb -- GitLab From 50d854e85c1c9b2db7b51002cbaf82844b776f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 13:21:51 +0200 Subject: [PATCH 0088/2403] fix remove license header line in binutils easyconfig --- .../easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 6923d84abe..037eea64d6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos +# License:: MIT/GPL # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -- GitLab From 8febcc4dcee4b8aa71bb8b6315bae23de1ef8f6f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 13:38:10 +1200 Subject: [PATCH 0089/2403] Added environment variable to force no CPU binding in Slurm --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 1 + .../easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 76be1035a7..1082a356d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -30,3 +30,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 3b66a977f7..4fa5665414 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -31,3 +31,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index c63048d89b..dc0616d42c 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 5a28bbce0d..b2f34f7977 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb index b63bd53de9..4c2e30db07 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -33,3 +33,4 @@ sanity_check_paths = { } moduleclass = 'chem' +modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From 29450f0d39654c8cf4ccaba1f97bab304e96d306 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jul 2015 15:57:32 +1200 Subject: [PATCH 0090/2403] ORCA 3.0.x is compiled against only OpenMPI 1.6.5 on linux --- ...nmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} | 6 ++-- .../ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb | 36 ------------------- ...PI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} | 6 ++-- ...PI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} | 6 ++-- 4 files changed, 7 insertions(+), 47 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64_openmpi_165.eb => ORCA-3_0_0-linux_x86-64.eb} (90%) delete mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_2-linux_x86-64.eb} (91%) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_3-linux_x86-64.eb} (91%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb similarity index 90% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 4fa5665414..1d969f2204 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,8 +1,7 @@ easyblock = "PackedBinary" name = "ORCA" -openmpiversion = '1.6.5' -version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) +version = '3_0_0-linux_x86-64' homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb deleted file mode 100644 index b2f34f7977..0000000000 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = "PackedBinary" - -name = "ORCA" -version = '3_0_2-linux_x86-64' - -openmpiversion = '1.8.1' -versionsuffix = '-OpenMPI-%s' % openmpiversion - -homepage = 'http://cec.mpg.de/forum/' -description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry - with specific emphasis on spectroscopic properties of open-shell molecules. - It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- - and multireference correlated ab initio methods. - It can also treat environmental and relativistic effects.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] - -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.8.3')] - -sanity_check_paths = { - 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + \ - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ - ['orca', 'otool_cosmo'], - 'dirs': [], -} - -moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index dc0616d42c..39d6350aed 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_2-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.2 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 4c2e30db07..adeb3b2fac 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -3,9 +3,6 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_3-linux_x86-64' -openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion - homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -17,7 +14,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] +# ORCA 3.0.3 is compiled only against OpenMPI 1.6.5 for Linux +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 38b7e620113a578a6ce459538610858fb6809fc2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 09:31:18 +0200 Subject: [PATCH 0091/2403] {tools}[intel/2015a] IPython 4.0.0 (WIP) --- ...IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..865d2c3f16 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,74 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '4.0.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +# this is a bundle of Python packages +# override extensions sanity check for IPython, importing a Python module doesn't work there +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s" || ipython -h', '') + +exts_list = [ + ('traitlets', '4.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pexpect', '3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('path.py', '7.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + }), + ('pickleshare', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('testpath', '0.2', { + 'source_urls': ['https://github.com/jupyter/testpath/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest', '')] + +moduleclass = 'tools' -- GitLab From 4c433fc27f1f85b4743387e68cdec549b5588596 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 09:48:14 +0200 Subject: [PATCH 0092/2403] fix exts_filter, enhance sanity check --- .../IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index 865d2c3f16..f5a2e2e413 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -25,7 +25,7 @@ dependencies = [ # this is a bundle of Python packages # override extensions sanity check for IPython, importing a Python module doesn't work there exts_defaultclass = 'PythonPackage' -exts_filter = ('python -c "import %(ext_name)s" || ipython -h', '') +exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('traitlets', '4.0.0', { @@ -56,6 +56,7 @@ exts_list = [ }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', }), ] @@ -65,10 +66,13 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} full_sanity_check = True sanity_check_paths = { - 'files': [], + 'files': [bin/ipython], 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest', '')] +sanity_check_commands = [ + ('ipython -h', ''), + ('iptest', ''), +] moduleclass = 'tools' -- GitLab From e63fc5d25f081b721910b1062526813c49a11b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 10:08:09 +0200 Subject: [PATCH 0093/2403] fix typo --- .../i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index f5a2e2e413..aee1a02648 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -66,7 +66,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} full_sanity_check = True sanity_check_paths = { - 'files': [bin/ipython], + 'files': ['bin/ipython'], 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -- GitLab From 06f61427222eaf3893ee869bb2dfcc885f49863e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 16:23:05 +0200 Subject: [PATCH 0094/2403] fix remarks --- .../CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 14 +++++++------- .../CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb index 6255d5289d..7ebcd2512d 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -3,18 +3,19 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'CONTRAlign' -version = '2.01-proteins' - easyblock = 'MakeCp' +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-proteins' + homepage = 'http://contra.stanford.edu/contralign/' -description = ''' CONditional TRAining for Protein Sequence Alignment ''' +description = """CONditional TRAining for Protein Sequence Alignment""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-proteins'))] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] patches = ['contralign-gcc47.patch'] @@ -24,8 +25,7 @@ start_dir = 'src' # Here we are compiling for protein input. Check docs for details makeopts = 'MODEL_TYPE="-DRNA=0"' -files_to_copy = [(['contralign', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/contralign'], diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb index 50d30ad789..bf7c0a545b 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -3,18 +3,19 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'CONTRAlign' -version = '2.01-rna' - easyblock = 'MakeCp' +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-rna' + homepage = 'http://contra.stanford.edu/contralign/' -description = ''' CONditional TRAining for Protein Sequence Alignment ''' +description = """CONditional TRAining for Protein Sequence Alignment""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_').strip('-rna'))] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] patches = ['contralign-gcc47.patch'] @@ -24,8 +25,7 @@ start_dir = 'src' # Here we are compiling for RNA input. Check docs for details makeopts = 'MODEL_TYPE="-DRNA=1"' -files_to_copy = [(['contralign', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/contralign'], -- GitLab From 105da2f6b4e12edd29a50d2d1bc144daa4be63c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 16:24:24 +0200 Subject: [PATCH 0095/2403] change name of patch file for CONTRAlign --- .../c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb | 2 +- .../c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb | 2 +- .../{contralign-gcc47.patch => CONTRAlign-2.01_gcc47.patch} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CONTRAlign/{contralign-gcc47.patch => CONTRAlign-2.01_gcc47.patch} (100%) diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb index 7ebcd2512d..84f7e76a78 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-proteins-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] -patches = ['contralign-gcc47.patch'] +patches = ['CONTRAlign-%(version)s_gcc47.patch'] start_dir = 'src' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb index bf7c0a545b..e483634c15 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-rna-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] -patches = ['contralign-gcc47.patch'] +patches = ['CONTRAlign-%(version)s_gcc47.patch'] start_dir = 'src' diff --git a/easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch similarity index 100% rename from easybuild/easyconfigs/c/CONTRAlign/contralign-gcc47.patch rename to easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch -- GitLab From b52b5f9dd4ae7a935bfebc2529857c32a51f536d Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 17:40:27 +0200 Subject: [PATCH 0096/2403] fixed identation --- .../l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb index e33c2344b7..df64a5cb98 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-goolf-1.4.10.eb @@ -2,8 +2,9 @@ name = 'libjpeg-turbo' version = '1.3.0' homepage = 'http://sourceforge.net/libjpeg-turbo/' -description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG -compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +description = """ libjpeg-turbo is a fork of the original IJG libjpeg which + uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg + is a library that implements JPEG image encoding, decoding and transcoding. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From a33824549b8b4d28dc203b289e9470c4ab80d279 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 17:48:48 +0200 Subject: [PATCH 0097/2403] switch to buildopts --- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb index f97abdf878..6a15dc9c32 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} source_urls = ['https://github.com/bedops/bedops/archive/'] sources = ['v%(version)s.tar.gz'] -makeopts = ' static && make install' +buildopts = ' static && make install' parallel = 1 -- GitLab From 7664abd5d65cd56d3e654dec8153f9b610382cac Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:01:45 +0200 Subject: [PATCH 0098/2403] file renamed --- .../{BEDOPS-2.4.1-GCC-4.8.2.eb => BEDOPS-2.4.1-GCC-4.8.4.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/BEDOPS/{BEDOPS-2.4.1-GCC-4.8.2.eb => BEDOPS-2.4.1-GCC-4.8.4.eb} (100%) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb similarity index 100% rename from easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.2.eb rename to easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb -- GitLab From d182c7f888b2660586c8274767c2398208591c6c Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:02:10 +0200 Subject: [PATCH 0099/2403] switchted to gcc-4.8.4 --- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb index 6a15dc9c32..47aaf73fa3 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -15,7 +15,7 @@ description = """ BEDOPS is an open-source command-line toolkit that performs hi # this application requires GCC-4.8.x or higher # be aware if you switch to a different toolchain -toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchain = {'name': 'GCC', 'version': '4.8.4'} source_urls = ['https://github.com/bedops/bedops/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 250219c48f3d03795f4875cb35c781c6b2fb0c98 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:23:08 +0200 Subject: [PATCH 0100/2403] switch to buildops and removed empty line --- .../m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb | 3 +-- .../m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb index afc62c9a6c..04ab889eab 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10_2014-04-25.eb @@ -25,7 +25,7 @@ parallel = 1 start_dir = "src" -makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb index 47308d8d3d..c0347a9308 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.25_2014-04-25.eb @@ -25,7 +25,7 @@ parallel = 1 start_dir = "src" -makeopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] @@ -35,4 +35,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 2cfb04cc3a8a161032657ee1f57a6720583ed747 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:27:53 +0200 Subject: [PATCH 0101/2403] switch to buildopts and added easyblock = 'ConfigureMake' --- .../easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb index c787473f52..435d596a7e 100644 --- a/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/Raster3D/Raster3D-3.0-2-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'Raster3D' version = '3.0-2' @@ -22,7 +24,7 @@ source_urls = [homepage] sources = ['%(name)s_%(version)s.tar.gz'] skipsteps = ['configure'] -makeopts = ' linux && make all' +buildopts = ' linux && make all' installopts = 'prefix=%(installdir)s' dependencies = [ -- GitLab From 767f0cd2afc2a621e7d2df61ee933c2fefdbe54c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 8 Oct 2015 08:17:16 +1300 Subject: [PATCH 0102/2403] Updated configuration file for new release of IMOD 4.7 --- ....12_RHEL6-64.eb => IMOD-4.7.15_RHEL6-64_CUDA6.0.eb} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/i/IMOD/{IMOD-4.7.12_RHEL6-64.eb => IMOD-4.7.15_RHEL6-64_CUDA6.0.eb} (86%) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb similarity index 86% rename from easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb rename to easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 1bf6bb89e6..7ada1695f6 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,7 +1,8 @@ easyblock = 'Binary' name = 'IMOD' -version = '4.7.12_RHEL6-64' +version = '4.7.15' +versionsuffix = '_RHEL6-64_CUDA6.0' homepage = 'http://bio3d.colorado.edu/imod/' description = """IMOD is a set of image processing, modeling and display @@ -14,11 +15,12 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'openmp': True} +dependencies = [('CUDA', '6.0.37')] source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] -sources = ['%(namelower)s_%(version)s.csh'] +sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] -install_cmd = "tcsh %(namelower)s_%(version)s.csh" +install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" # -dir: Choose location of installation directory # -skip: do not attempt to deploy resource files in /etc @@ -29,7 +31,7 @@ installopts = "-dir %(installdir)s -skip -yes" # like /usr/local. So it prefixes the install location with a lot of specific # directories that are surplus to requirements. postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s" ] sanity_check_paths = { -- GitLab From 9f185b43cf9bf44d3d34cc79627508acff8a92d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 30 Oct 2015 12:38:28 +1300 Subject: [PATCH 0103/2403] New easyconfig for DFT-D3 --- .../d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb new file mode 100644 index 0000000000..b28f706ce6 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.1.1' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] +sources = ['dftd3.tgz'] + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 339843c8214e538e3e4504fa272cf25d44f2db1f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Nov 2015 11:22:04 +1300 Subject: [PATCH 0104/2403] Added MD5 checksum for tarball --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index b28f706ce6..79b12d07a2 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] sources = ['dftd3.tgz'] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From 32b45df226ff531865587b3eecec0052f31aa491 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Nov 2015 11:31:07 +1300 Subject: [PATCH 0105/2403] Reformatted --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 7ada1695f6..100020fb13 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -41,11 +41,13 @@ sanity_check_paths = { # Assuming the system java /usr/java can be used. If not, we can # cross that bridge. -moduleclass = 'vis' -modextravars = {'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : "/usr/java", - 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", - 'FOR_DISABLE_STACK_TRACE' : 1, - 'IMOD_QTLIBDIR' : "$root/qtlib"} +modextravars = { + 'IMOD_DIR' : "$root", + 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", + 'FOR_DISABLE_STACK_TRACE' : 1, + 'IMOD_QTLIBDIR' : "$root/qtlib" +} modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" +moduleclass = 'vis' -- GitLab From 5b0c0c1ee7b7cc67844e081725158d40f8bcaae4 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 23 Dec 2015 16:05:31 +1300 Subject: [PATCH 0106/2403] New EasyConfig for GROMACS 5.0.7 --- .../GROMACS-5.0.7-intel-2015a-hybrid.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..69bf5a5d40 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.7' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 57f73ac1adc543a5a4e1e378bf2c6703eefa2728 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 6 Jan 2016 13:25:32 +1300 Subject: [PATCH 0107/2403] Comment out checksum, rename source file and add an explanatory comment --- .../easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 79b12d07a2..54c92da4c6 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -9,8 +9,13 @@ description = """DFT-D3 implements a dispersion correction for density functiona toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] -sources = ['dftd3.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball, and the +# checksum input has been disabled. +sources = ['dftd3-%(version)s.tgz'] +#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From 46360b0cde6acaa58abbe2df35be0ba027a59670 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 Jan 2016 14:03:17 +0100 Subject: [PATCH 0108/2403] {bio}[intel-2015b] GROMACS 5.1.1 (WIP) --- .../GROMACS-5.1.1-intel-2015b-hybrid.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb new file mode 100644 index 0000000000..327b471426 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.1.1' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.3.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.59.0', '-Python-2.7.10')] + +moduleclass = 'bio' -- GitLab From a5965e7a9e0133e17be5fbc26bfa677b98690222 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 26 Jan 2016 10:46:13 +1300 Subject: [PATCH 0109/2403] Re-enable checksum verification --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 54c92da4c6..3ea34a9824 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -12,10 +12,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this -# reason, it is suggested to manually download and rename the tarball, and the -# checksum input has been disabled. +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. sources = ['dftd3-%(version)s.tgz'] -#checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From d2838453775eea122fc9e83d88c597679979f10a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 26 Jan 2016 12:06:24 +1300 Subject: [PATCH 0110/2403] Add Java as a dependency --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 28 +++++++++++++------ 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 100020fb13..56dc7ea9cd 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -15,11 +15,18 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'openmp': True} -dependencies = [('CUDA', '6.0.37')] source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] +java = 'Java' +javaver = '1.8.0_40' + +dependencies = [ + ('CUDA', '6.0.37'), + (java, javaver), +] + install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" # -dir: Choose location of installation directory @@ -28,26 +35,29 @@ install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" installopts = "-dir %(installdir)s -skip -yes" # The assumption by the install script is that installdir will be something -# like /usr/local. So it prefixes the install location with a lot of specific -# directories that are surplus to requirements. -postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s" - ] +# like /usr/local. So it creates, within the specified install location, a +# number of additional directories within which to install IMOD. We will, +# therefore, move the contents of these directories up and throw away the +# directories themselves. Doing so apparently is not a problem so long as +# IMOD_DIR (see below) is correctly set in the module. +postinstallcmds = [ + "mv %(installdir)s/%(name)s/* %(installdir)s/.", + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s", +] sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], 'dirs': ['bin', 'lib'] } -# Assuming the system java /usr/java can be used. If not, we can -# cross that bridge. modextravars = { 'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_JAVADIR' : os.getenv('EBROOTJAVA'), 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", 'FOR_DISABLE_STACK_TRACE' : 1, 'IMOD_QTLIBDIR' : "$root/qtlib" } modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" + moduleclass = 'vis' -- GitLab From d20fd461af0643a43a7e80b8cc740aa480f45276 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 2 Feb 2016 14:18:16 +1300 Subject: [PATCH 0111/2403] New EasyConfig for GDAL 2.0.1 with the foss-2015a toolchain --- .../g/GDAL/GDAL-2.0.1-foss-2015a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb new file mode 100644 index 0000000000..fdbd875ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.1' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('KEALib', '1.4.4'), + ('netCDF', '4.3.3.1'), + ('HDF5', '1.8.16'), + ('expat', '2.1.0'), + ('libxml2', '2.9.3', '-Python-2.7.11'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' -- GitLab From 53f6520880cc45a7b2e7445b6e4b08f5567a386e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 09:41:43 +0100 Subject: [PATCH 0112/2403] added latest spades easyconfig --- .../s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..df5ad900a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.6.2' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """ Genome assembler for single-cell and isolates data sets """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '2.8.12')] + +dependencies = [('zlib', '1.2.8')] + +start_dir = 'src' + +separate_build_dir = True + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bwa-spades", "dipspades", "dipspades.py", + "hammer", "ionhammer", "spades", "spades.py"]], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 2c80f6c053b517e747b5d256a6768ce7084fcb18 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 09:43:43 +0100 Subject: [PATCH 0113/2403] updated header --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb index df5ad900a5..95828fbb10 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics easyblock = "CMakeMake" -- GitLab From 456825c036b0f2a829126d009979b985d4d3f8c4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 4 Feb 2016 18:16:42 +0100 Subject: [PATCH 0114/2403] style fixes --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb index 95828fbb10..b09bce53d6 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -9,7 +9,7 @@ name = 'SPAdes' version = '3.6.2' homepage = 'http://bioinf.spbau.ru/en/spades' -description = """ Genome assembler for single-cell and isolates data sets """ +description = """Genome assembler for single-cell and isolates data sets""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From e472f51b95ce4d6299d3855ac6b59feecaa950da Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 8 Feb 2016 23:35:55 +0100 Subject: [PATCH 0115/2403] latest IPython and all the dependencies --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 161 ++++++++++++++++++ ...Q-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb | 33 ++++ .../util-linux-2.26.1-goolf-1.4.10.eb | 33 ++++ .../z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb | 34 ++++ 4 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..87c223eb01 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,161 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.1.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('setuptools', '19.6', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.14.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.10.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-1.10.1.tar.bz2', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-0.8.1.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pickleshare', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('pbr', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + }), + ('notebook', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pyzmq', '15.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'modulename': 'zmq', + }), + #('testpath', '0.3', { + #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) + #'source_tmpl': '0.3.tar.gz', + #}), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + #('iptest', ''), # this test fails with 'ImportError: No module named testpath'. testpath cannot be installed with easyconfig + #('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb new file mode 100644 index 0000000000..f2939de491 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-goolf-1.4.10-Python-2.7.5-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.5' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..dec0e334ca --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..a6ea95a4c2 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 931b9a9f5728494b315e920938340b400af4dedc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 11:15:34 +0100 Subject: [PATCH 0116/2403] removed PyZMQ from exts_list. Provided as dependency --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 87c223eb01..f745db8910 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -130,10 +130,6 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), - ('pyzmq', '15.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], - 'modulename': 'zmq', - }), #('testpath', '0.3', { #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) #'source_tmpl': '0.3.tar.gz', -- GitLab From c74a8a203fbb60fe2448b7dc3a7fb6340bd6642f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 20:30:39 +0100 Subject: [PATCH 0117/2403] added sqlite dep --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index f745db8910..6b7bb08515 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,6 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), + ('SQLite', '3.8.1'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] -- GitLab From 7b71fbdc8c2d229b1e9bab1cf27187d8f688cfa9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 9 Feb 2016 21:19:25 +0100 Subject: [PATCH 0118/2403] updated sqlite dep --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 6b7bb08515..af763e233d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,7 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), - ('SQLite', '3.8.1'), + ('SQLite', '3.8.10.2'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] -- GitLab From 28e16800c2f64d02b6846ee2aaac88f1719bf719 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 12 Feb 2016 16:11:23 +0100 Subject: [PATCH 0119/2403] added git-lfs easyconfig --- .../easyconfigs/g/git-lfs/git-lfs-1.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb new file mode 100755 index 0000000000..2baa195a5a --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'git-lfs' +version = '1.1.1' + +homepage = 'https://git-lfs.github.com/' +description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, + datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server + like GitHub.com or GitHub Enterprise.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/github/git-lfs/releases/download/v%(version)s/'] +sources = ['%(name)s-linux-amd64-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ["git-lfs"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', + } + +# delete to provide installation script +postinstallcmds = ["rm -fr %(installdir)s/install.sh"] + +moduleclass = 'tools' -- GitLab From cdf12d46eff5743af67cf80615ac0800ce10c11a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 16 Feb 2016 12:08:41 +1300 Subject: [PATCH 0120/2403] Add RSH_COMMAND variable to module files for ORCA --- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 6 +++++- easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb | 6 +++++- 4 files changed, 20 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 1082a356d5..1f68602fad 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -29,5 +29,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index 1d969f2204..976f97b5d5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 39d6350aed..e21c8f3ed4 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index adeb3b2fac..547be86ff0 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -30,5 +30,9 @@ sanity_check_paths = { 'dirs': [], } +modextravars = { + "SLURM_CPU_BIND" : "none", + "RSH_COMMAND" : "ssh -x", +} + moduleclass = 'chem' -modextravars = { "SLURM_CPU_BIND" : "none" } -- GitLab From 829d4bce5aa38d6444c4eb516969f6264205b4d3 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 18 Feb 2016 13:33:41 +1300 Subject: [PATCH 0121/2403] Reinstate Open MPI version --- easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb index bd3a091b31..9110e61a28 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb @@ -1,7 +1,8 @@ easyblock = "PackedBinary" name = "ORCA" -version = '3_0_0-linux_x86-64' +openmpiversion = '1.6.5' +version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -15,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] # ORCA 3.0.0 is compiled only against OpenMPI 1.6.5 for Linux -dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From c08bd4a87dc921af2bf10fe29a6f8a604787ddeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:19:42 +0100 Subject: [PATCH 0122/2403] {toolchain}[dummy] intel 2016.02 --- .../easyconfigs/i/intel/intel-2016.02.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.02.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb new file mode 100644 index 0000000000..4c2ff105d6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -0,0 +1,25 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'intel' +version = '2016.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.2.181' +gccver = '4.9.3' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 3807a518db8659408f9261906b69c3a819a3b98f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 20:55:57 +0100 Subject: [PATCH 0123/2403] bump GCC to 5.3.0 --- easybuild/easyconfigs/i/intel/intel-2016.02.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02.eb index 4c2ff105d6..47932a57f9 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02.eb @@ -10,7 +10,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '4.9.3' +gccver = '5.3.0' binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From 0907ea3fd1c6bbeaeb6064ba47eddb79851b6551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Feb 2016 23:12:00 +0100 Subject: [PATCH 0124/2403] {compiler}[dummp] GCC 5.3.0-2.26 --- .../b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb | 27 + .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 41 + .../easyconfigs/b/binutils/binutils-2.26.eb | 39 + .../f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 16 + easybuild/easyconfigs/f/flex/flex-2.6.0.eb | 16 + easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb | 25 + .../easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 +- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 54 + .../mpfr-3.1.3-allpatches-20151029.patch | 1830 +++++++++++++++++ .../m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 26 + .../z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 25 + 11 files changed, 2100 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..b7cebec049 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..ca71c5f04e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb new file mode 100644 index 0000000000..5145e1becd --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +# statically link with zlib, to avoid runtime dependency on zlib +# further, add the system library path in the rpath: this should 'harden' the +# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +prebuildopts = preconfigopts + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f20e1d0126 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb new file mode 100644 index 0000000000..e7580df4ae --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -0,0 +1,16 @@ +name = 'flex' +version = '2.6.0' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..34bf1f36a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.3.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..40449db3d5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -10,7 +10,6 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -gcc_name = 'GCC' source_urls = [ 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror @@ -19,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ - '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gcc-%(version)s.tar.bz2', 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.2.tar.gz', diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb new file mode 100644 index 0000000000..e7aac86863 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20151029.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch new file mode 100644 index 0000000000..891831f521 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.3-allpatches-20151029.patch @@ -0,0 +1,1830 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("d1 or (np[n-1]=d1 and np[n-2]>=d0) here, ++ since we truncate the divisor at each step, but since {np,n} < D ++ originally, the largest possible partial quotient is B-1. */ ++ if (MPFR_UNLIKELY(np[n-1] > d1 || (np[n-1] == d1 && np[n-2] >= d0))) + q2 = ~ (mp_limb_t) 0; + else + udiv_qr_3by2 (q2, q1, q0, np[n - 1], np[n - 2], np[n - 3], +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-17 08:58:21.118986898 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-10-29 13:47:46.763900609 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p4"; ++ return "3.1.3-p5"; + } +diff -Naurd mpfr-3.1.3-a/tests/tdiv.c mpfr-3.1.3-b/tests/tdiv.c +--- mpfr-3.1.3-a/tests/tdiv.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tdiv.c 2015-10-29 13:47:46.751900855 +0000 +@@ -1099,6 +1099,69 @@ + mpfr_set_emax (old_emax); + } + ++/* Bug in mpfr_divhigh_n_basecase when all limbs of q (except the most ++ significant one) are B-1 where B=2^GMP_NUMB_BITS. Since we truncate ++ the divisor at each step, it might happen at some point that ++ (np[n-1],np[n-2]) > (d1,d0), and not only the equality. ++ Reported by Ricky Farr ++ ++ To get a failure, a MPFR_DIVHIGH_TAB entry below the MPFR_DIV_THRESHOLD ++ limit must have a value 0. With most mparam.h files, this cannot occur. */ ++static void ++test_20151023 (void) ++{ ++ mpfr_prec_t p; ++ mpfr_t n, d, q, q0; ++ int inex, i; ++ ++ for (p = GMP_NUMB_BITS; p <= 2000; p++) ++ { ++ mpfr_init2 (n, 2*p); ++ mpfr_init2 (d, p); ++ mpfr_init2 (q, p); ++ mpfr_init2 (q0, GMP_NUMB_BITS); ++ ++ /* generate a random divisor of p bits */ ++ mpfr_urandomb (d, RANDS); ++ /* generate a random quotient of GMP_NUMB_BITS bits */ ++ mpfr_urandomb (q0, RANDS); ++ /* zero-pad the quotient to p bits */ ++ inex = mpfr_prec_round (q0, p, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ ++ for (i = 0; i < 3; i++) ++ { ++ /* i=0: try with the original quotient xxx000...000 ++ i=1: try with the original quotient minus one ulp ++ i=2: try with the original quotient plus one ulp */ ++ if (i == 1) ++ mpfr_nextbelow (q0); ++ else if (i == 2) ++ { ++ mpfr_nextabove (q0); ++ mpfr_nextabove (q0); ++ } ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextabove (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ ++ inex = mpfr_mul (n, d, q0, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_nextbelow (n); ++ mpfr_div (q, n, d, MPFR_RNDN); ++ MPFR_ASSERTN(mpfr_cmp (q, q0) == 0); ++ } ++ ++ mpfr_clear (n); ++ mpfr_clear (d); ++ mpfr_clear (q); ++ mpfr_clear (q0); ++ } ++} ++ + #define TEST_FUNCTION test_div + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -1219,6 +1282,7 @@ + consistency (); + test_20070603 (); + test_20070628 (); ++ test_20151023 (); + test_generic (2, 800, 50); + test_extreme (); + diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..0a925c97ef --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..f4a9aac776 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From d67d88a99ac9860c6a57151d3c5ce24e73c20c7f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 19 Feb 2016 15:37:10 +1300 Subject: [PATCH 0125/2403] Rename ORCA-3.0.0 EasyConfig to that which is expected given version string --- ...0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} (100%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb similarity index 100% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb -- GitLab From b0d79ea7c64b6afd599aed88c22d3eef04509edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Feb 2016 19:23:16 +0100 Subject: [PATCH 0126/2403] non-parallel build of flex 2.6.0 --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index f20e1d0126..0c9f4d80a4 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,4 +13,6 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +parallel = 1 + moduleclass = 'lang' -- GitLab From bdb97bbfc198c2a62a7c2170bd01bf7f9b836c28 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 21 Feb 2016 18:21:45 +0100 Subject: [PATCH 0127/2403] fix readline dependency conflict --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 6a41f5863c..7b7e716a53 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -26,7 +26,7 @@ version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.spl sources = ['sqlite-autoconf-%s.tar.gz' % version_str] dependencies = [ - ('libreadline', '6.3'), + ('libreadline', '6.2'), ('Tcl', '8.6.4'), ] -- GitLab From 48e5277f12e469d1e17d5a779e8946242d944d8d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Feb 2016 15:11:38 +0100 Subject: [PATCH 0128/2403] CP2k 3.0 for intel/2016a --- .../c/CP2K/CP2K-3.0-intel-2016a.eb | 38 +++++++++++++++++++ .../l/Libint/Libint-1.1.4-intel-2016a.eb | 24 ++++++++++++ .../l/libxc/libxc-2.2.2-intel-2016a.eb | 32 ++++++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb new file mode 100644 index 0000000000..9d0e4f481b --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '3.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..61a5c02419 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb new file mode 100644 index 0000000000..959f0d1356 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From ac629d4ead19313901dfaca5df599618a24d5430 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Feb 2016 15:12:10 +0100 Subject: [PATCH 0129/2403] psmp build of CP2k --- .../c/CP2K/CP2K-3.0-intel-2016a-psmp.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb new file mode 100644 index 0000000000..a3380d03a5 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb @@ -0,0 +1,42 @@ +name = 'CP2K' +version = '3.0' +versionsuffix = '-psmp' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +# ('FFTW', '3.3.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +type = 'psmp' + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' -- GitLab From 992f0591971ca3c922def68b7ab40e1556b40853 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:13:55 +1300 Subject: [PATCH 0130/2403] New EasyConfig for non-Python version of libxml2 2.9.3 with the foss 2015a toolchain --- .../l/libxml2/libxml2-2.9.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb new file mode 100644 index 0000000000..7c1a817fb6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [ + ('zlib', '1.2.8'), +] + +moduleclass = 'lib' -- GitLab From 3021683dd3556e76a3a06e229d4e338153d82764 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 24 Feb 2016 14:22:59 +1300 Subject: [PATCH 0131/2403] No longer require python bindings for libxml2 dependency --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb index fdbd875ff2..001e2879da 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.1-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('netCDF', '4.3.3.1'), ('HDF5', '1.8.16'), ('expat', '2.1.0'), - ('libxml2', '2.9.3', '-Python-2.7.11'), + ('libxml2', '2.9.3'), ('zlib', '1.2.8'), ] -- GitLab From 42b700b5c1f404196aab8dc21c1f1159caad949e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2016 17:05:37 +0200 Subject: [PATCH 0132/2403] add easyconfig nco-0.0.2-intel-2016a-Python-2.7.11.eb --- .../nco-0.0.2-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0732494447 --- /dev/null +++ b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'nco' +version = '0.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nco/pynco' +description = """Python bindings for NCO""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('NCO', '4.4.9', versionsuffix), + ('numpy', '1.10.4', versionsuffix), + ('scipy', '0.16.1', versionsuffix), + ('netcdf4-python', '1.2.2', versionsuffix), + +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From b0d06e61a6bb264589f31d972212e831480b7c76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 17:56:10 +0100 Subject: [PATCH 0133/2403] add binutils as dependency in flex easyconfig --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 0c9f4d80a4..e1a9437774 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -13,6 +13,9 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] dependencies = [('Bison', '3.0.4')] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + parallel = 1 moduleclass = 'lang' -- GitLab From b28601235af520ecfd1a97b6375802e123717d2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Feb 2016 21:04:26 +0100 Subject: [PATCH 0134/2403] add icc/ifort/impi/imkl easyconfigs for intel/2016.02 + HPL as testcase --- .../h/HPL/HPL-2.1-intel-2016.02.eb | 18 +++++++++ .../i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 18 +++++++++ .../ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ .../i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb | 22 +++++++++++ ...11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 38 +++++++++++++++++++ ....181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 34 +++++++++++++++++ 7 files changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb new file mode 100644 index 0000000000..f4c0fccb16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.02'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..f4abc8bef2 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..e07e4371a2 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.2.181' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..916145cd26 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.2.181' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..9e93414ff1 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.02' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.181' +compver = '2016.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..74cc4cff3a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..ef29e9af70 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -0,0 +1,34 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' -- GitLab From 1fd2f757002f308e9a18d8da6607d72be91112fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 21:55:51 +0000 Subject: [PATCH 0135/2403] Port TopHat2 to foss-2015b --- .../t/TopHat/TopHat-2.1.1-foss-2015b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb new file mode 100644 index 0000000000..31db65ea57 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat_ictce.patch', + 'tophat-2.0.13-zlib.patch', +] + +dependencies = [ + ('Boost', '1.60.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 78dc6d965f6ee331912f3d693fbb044ce7e713db Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:03:45 +0000 Subject: [PATCH 0136/2403] Disable obsolete bundled SeqAn patch for ictce --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index 31db65ea57..dfc3160664 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - 'tophat_ictce.patch', + #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From 2a49fc45bee7a42924637dc5db55c101d5081b91 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 28 Feb 2016 22:06:27 +0000 Subject: [PATCH 0137/2403] Remove reference to obsolete patch --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index dfc3160664..3bdcb05552 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -20,7 +20,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = [ - #'tophat_ictce.patch', 'tophat-2.0.13-zlib.patch', ] -- GitLab From cf8af929948aab0e69ac63c4a69a2ca95d097779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 18:31:30 +0100 Subject: [PATCH 0138/2403] {numlib}[intel/2016a] CGAL 4.7 (WIP) --- .../CGAL-4.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1e7bf4a653 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] + + +mesaver = '11.1.2' +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.3', '-GMP-6.1.0'), + ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), + ('Mesa', mesaver, versionsuffix), + ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' -- GitLab From a13cd4a58ec6afa53a1a94456cde5b0132321982 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:56:21 +0100 Subject: [PATCH 0139/2403] fix binutils version in M4 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 0a925c97ef..434b6f02ff 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.26', '', True)] configopts = "--enable-cxx" -- GitLab From 56f9e64c25579bf780f1673462c44839ef9b62ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 19:57:44 +0100 Subject: [PATCH 0140/2403] fix source URL for GCC tarball in GCCcore easyconfig --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index e7aac86863..1f2fc04edb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official -- GitLab From adbae798a1cb89db32c3a047537bb6f2318ae7c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Feb 2016 20:17:02 +0100 Subject: [PATCH 0141/2403] add clarifying comment --- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 1 + 8 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 7354472c7e..17d0ffe45a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index c6144a5afd..e56edba4db 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 0748e2d400..d80f4b798c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index f4abc8bef2..080cfccc9a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index c188753ac5..b41f57ab66 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index b01714a6f5..c64470205a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -12,6 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index f961cef224..4e5be0a9bb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 916145cd26..3ee926155e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -21,6 +21,7 @@ dependencies = [ ('binutils', binutilsver, '', ('GCCcore', gccver)), ] +# list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -- GitLab From 03e8089e885b5067fd74b9e361bc7ce43a1ae062 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 20:21:03 +0100 Subject: [PATCH 0142/2403] adding python 2.7.11 craygnu as used by CSCS --- .../freetype-2.5.5-CrayGNU-2015.11-XC.eb | 22 ++++++ .../libpng-1.6.16-CrayGNU-2015.11-XC.eb | 19 +++++ .../ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb | 20 +++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 75 +++++++++++++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..5231cd9418 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..6191aef3b9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--disable-static" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..ac14395c2f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,20 @@ +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files' : ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses6-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + ['lib/lib%s.a' % x for x in ["form", "form", "menu", "menu_g", "ncurses", "ncurses++", "ncurses_g", "panel", "panel_g"]], + 'dirs' : ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..73a8ef05b0 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -0,0 +1,75 @@ +# contributed by Luca MArsella and GPPezzi (CSCS) + +name = 'Python' +version = "2.7.11" + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'dynamic': True, 'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +patches = ['unixccompiler-Python-2.7.9.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +osdependencies = [('libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Mar 1st 2016 +exts_list = [ + ('setuptools', '20.2.2', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.3', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), + ('matplotlib', '1.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + }), +] + +moduleclass = 'lang' -- GitLab From c0ab8886803c3276ff804174ef73fcaae9a8c56e Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 20:25:25 +0100 Subject: [PATCH 0143/2403] adding patch --- .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 2 +- .../p/Python/unixccompiler-Python-2.7.11.patch | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 73a8ef05b0..58773af2db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -15,7 +15,7 @@ scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['unixccompiler-Python-2.7.9.patch'] +patches = ['unixccompiler-Python-2.7.11.patch'] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch b/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch new file mode 100644 index 0000000000..b0b4febb27 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/unixccompiler-Python-2.7.11.patch @@ -0,0 +1,11 @@ +--- EasyBuildTesting/Python-2.7.9/Lib/distutils.orig/unixccompiler.py 2014-12-10 16:59:34.000000000 +0100 ++++ EasyBuildTesting/Python-2.7.9/Lib/distutils/unixccompiler.py 2015-06-12 16:02:06.000000000 +0200 +@@ -237,7 +237,7 @@ + elif self._is_gcc(compiler): + return "-Wl,-R" + dir + else: +- return "-R" + dir ++ return "-Wl,-R " + dir + + def library_option(self, lib): + return "-l" + lib -- GitLab From ee240ae136ccae9728c02f9ea66c4efd1f51715e Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 1 Mar 2016 22:18:41 +0100 Subject: [PATCH 0144/2403] ncurses 5.9 --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 58773af2db..e7139b7c31 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -22,7 +22,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), ('libreadline', '6.3'), - ('ncurses', '6.0'), + ('ncurses', '5.9'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), ] -- GitLab From 6705f22d89a2e38e66fa5f7a2a65c4a518ed0979 Mon Sep 17 00:00:00 2001 From: Guilherme Date: Tue, 1 Mar 2016 22:25:20 +0100 Subject: [PATCH 0145/2403] Delete ncurses-6.0-CrayGNU-2015.11-XC.eb --- .../ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb deleted file mode 100644 index ac14395c2f..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2015.11-XC.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'ncurses' -version = '6.0' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files' : ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses6-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + ['lib/lib%s.a' % x for x in ["form", "form", "menu", "menu_g", "ncurses", "ncurses++", "ncurses_g", "panel", "panel_g"]], - 'dirs' : ['include'] -} - -moduleclass = 'devel' -- GitLab From 3d46bcfd86d9d374e5218083ef4f2ce80d3da28a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 2 Mar 2016 15:11:31 +1300 Subject: [PATCH 0146/2403] Move things into the EasyBlock --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 56dc7ea9cd..0f356768c8 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,5 +1,3 @@ -easyblock = 'Binary' - name = 'IMOD' version = '4.7.15' versionsuffix = '_RHEL6-64_CUDA6.0' @@ -27,37 +25,4 @@ dependencies = [ (java, javaver), ] -install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" - -# -dir: Choose location of installation directory -# -skip: do not attempt to deploy resource files in /etc -# -yes: do not prompt for confirmation -installopts = "-dir %(installdir)s -skip -yes" - -# The assumption by the install script is that installdir will be something -# like /usr/local. So it creates, within the specified install location, a -# number of additional directories within which to install IMOD. We will, -# therefore, move the contents of these directories up and throw away the -# directories themselves. Doing so apparently is not a problem so long as -# IMOD_DIR (see below) is correctly set in the module. -postinstallcmds = [ - "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s", -] - -sanity_check_paths = { - 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], - 'dirs': ['bin', 'lib'] -} - -modextravars = { - 'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : os.getenv('EBROOTJAVA'), - 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", - 'FOR_DISABLE_STACK_TRACE' : 1, - 'IMOD_QTLIBDIR' : "$root/qtlib" -} -modaliases = {'subm' : "submfg $* &"} -modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" - moduleclass = 'vis' -- GitLab From 5db02000b88668f2e7d23d4bc0f6806e6cff699c Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 14:08:29 +0100 Subject: [PATCH 0147/2403] h5py CrayGNU Python 2.7.11 2015.11-XC --- ...ayGNU-2015.11-XC-Python-2.7.11-parallel.eb | 28 ++++++++++++++++ ...CrayGNU-2015.11-XC-Python-2.7.11-serial.eb | 33 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb new file mode 100644 index 0000000000..c3c38a4d6a --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb @@ -0,0 +1,28 @@ +easyblock = "h5py" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[0:2]) +hdf5suff = '-parallel' +versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) + +dependencies = [ + (python, pyver), + ('cray-hdf5-parallel/1.8.14', EXTERNAL_MODULE), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb new file mode 100644 index 0000000000..31eb53599d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[0:2]) +hdf5suff = '-serial' +versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) + +dependencies = [ + (python, pyver), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], +} + +moduleclass = 'data' -- GitLab From d4141f21b9773340d98087b24e8378c125ff8785 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 14:51:23 +0100 Subject: [PATCH 0148/2403] minor fixes --- .../h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb | 5 +++++ .../h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb | 1 - 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb index c3c38a4d6a..83499c5b4e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb @@ -25,4 +25,9 @@ dependencies = [ ('cray-hdf5-parallel/1.8.14', EXTERNAL_MODULE), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb index 31eb53599d..131a99a851 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb @@ -9,7 +9,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From 2ccf836645880dfe1416b2b5f67b90938d4d8ee9 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 15:15:03 +0100 Subject: [PATCH 0149/2403] boost craygnu python 2.7.11 --- ...1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb new file mode 100644 index 0000000000..5be4348909 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -0,0 +1,29 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'boostcray' + +name = 'Boost' +version = "1.60.0" + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.bz2' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From 055f6e3cacbfa430dea59018eec1a5343bf5182b Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 16:53:46 +0100 Subject: [PATCH 0150/2403] updated to avoid need of easyblock --- .../h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb index 83499c5b4e..2b67f8581d 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb @@ -1,4 +1,5 @@ -easyblock = "h5py" +easyblock = "PythonPackage" +#easyblock = "h5py" name = 'h5py' version = '2.5.0' @@ -14,6 +15,8 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +prebuildopts = ' python setup.py configure --mpi && ' + python = 'Python' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[0:2]) -- GitLab From ef98f2ef09dc644655b276bda9885cde6b27d8f8 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 16:55:57 +0100 Subject: [PATCH 0151/2403] minor --- .../h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb index 2b67f8581d..fc52ac2162 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb @@ -1,5 +1,4 @@ easyblock = "PythonPackage" -#easyblock = "h5py" name = 'h5py' version = '2.5.0' -- GitLab From 42f838992f1526a957c91a6f05161466394b3636 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Mar 2016 18:43:11 +0100 Subject: [PATCH 0152/2403] rename to intel/2016.02-GCC-5.3 --- ...1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} | 2 +- .../i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-intel-2016.02.eb => HPL-2.1-intel-2016.02-GCC-5.3.eb} (91%) rename easybuild/easyconfigs/i/intel/{intel-2016.02.eb => intel-2016.02-GCC-5.3.eb} (85%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb similarity index 91% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index f4c0fccb16..ffa453cdb4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2016.02'} +toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb similarity index 85% rename from easybuild/easyconfigs/i/intel/intel-2016.02.eb rename to easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 47932a57f9..4d1e0dddac 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -1,8 +1,9 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild -easyblock = "Toolchain" +easyblock = 'Toolchain' name = 'intel' version = '2016.02' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" @@ -10,7 +11,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.2.181' -gccver = '5.3.0' +gccver = '%s.0' % gcc_maj_min binutilsver = '2.26' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From b8e4a25cec60fe50c037e9614ac6d497a916b47e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 18:09:15 +0000 Subject: [PATCH 0153/2403] First version of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb new file mode 100644 index 0000000000..245a7b2f5a --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -0,0 +1,30 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# It was auto-generated based on a template easyconfig, so it should be used with care. +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0p1' + +homepage = 'http://subread.sourceforge.net/' +description = """TEMPLATE DESCRIPTION""" + +# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ +sources = ['%(namelower)s-%version)s-source.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +dependencies = [] + +# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From 47ab1fb40686dadb3001e5550adc513d8509f212 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 20:14:01 +0100 Subject: [PATCH 0154/2403] fix remark --- .../h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb index fc52ac2162..4422d5da72 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb @@ -14,8 +14,6 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -prebuildopts = ' python setup.py configure --mpi && ' - python = 'Python' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[0:2]) @@ -27,6 +25,8 @@ dependencies = [ ('cray-hdf5-parallel/1.8.14', EXTERNAL_MODULE), ] +prebuildopts = ' python setup.py configure --mpi && ' + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], -- GitLab From f038794ebafd3137021e07532136e6b116b631ce Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Mar 2016 21:43:15 +0000 Subject: [PATCH 0155/2403] Add first draft of RSeQC including numpy dep --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ++++++++++++++ .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..f55df325cf --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,27 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb new file mode 100644 index 0000000000..c0f1f917f6 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '2.6.3' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [] + +Python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + ('R', '3.2.3'), + ('numpy', '1.9.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From ff5e2fde5d662b1f667c5a4268d029d98a49eaf8 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 2 Mar 2016 22:44:24 +0100 Subject: [PATCH 0156/2403] fixed remarks and separated matplot lib as independent module --- ...b => freetype-2.6.2-CrayGNU-2015.11-XC.eb} | 5 +- ...eb => libpng-1.6.21-CrayGNU-2015.11-XC.eb} | 6 +- ...-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb | 45 ++++++++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 89 +++++++++++++++---- 4 files changed, 123 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.5.5-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11-XC.eb} (88%) rename easybuild/easyconfigs/l/libpng/{libpng-1.6.16-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11-XC.eb} (77%) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb similarity index 88% rename from easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb index 5231cd9418..97d02aea84 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb @@ -1,5 +1,5 @@ name = 'freetype' -version = '2.5.5' +version = '2.6.2' homepage = 'http://freetype.org' description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and @@ -7,12 +7,11 @@ description = """FreeType 2 is a software font engine that is designed to be sma servers, font conversion tools, text image generation tools, and many other products as well.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.16')] +dependencies = [('libpng', '1.6.21')] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb similarity index 77% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb index 6191aef3b9..f58ee3b579 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb @@ -1,19 +1,17 @@ easyblock = 'ConfigureMake' name = 'libpng' -version = '1.6.16' +version = '1.6.21' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.8')] -configopts = "--disable-static" - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb new file mode 100644 index 0000000000..9a9609ca9e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c "import %(ext_name)s"', '') + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index e7139b7c31..0169075b4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -1,4 +1,4 @@ -# contributed by Luca MArsella and GPPezzi (CSCS) +# contributed by Luca Marsella and GPPezzi (CSCS) name = 'Python' version = "2.7.11" @@ -7,7 +7,7 @@ homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} -toolchainopts = {'dynamic': True, 'pic': True, 'opt': True, 'optarch': True} +toolchainopts = {'pic': True} numpyversion = '1.10.4' scipyversion = '0.16.1' @@ -23,25 +23,21 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - ('freetype', '2.5.5'), - ('libpng', '1.6.16'), ] -osdependencies = [('libopenssl-devel')] - -buildopts = 'LINKCC="$CC -dynamic"' +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # order is important! # package versions updated Mar 1st 2016 exts_list = [ ('setuptools', '20.2.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '8.0.3', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.7', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,24 +47,87 @@ exts_list = [ }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), ('Cython', '0.23.4', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('virtualenv', '14.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('matplotlib', '1.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), ] -- GitLab From be7882c7c86d1265dbaea105e03db457b48159de Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 3 Mar 2016 17:15:30 +0100 Subject: [PATCH 0157/2403] added sanity check for libpng --- .../l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb | 7 +++++++ .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 + 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb index f58ee3b579..bb061f924f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb @@ -14,4 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.8')] +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 0169075b4a..7eef88d995 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -15,6 +15,7 @@ scipyversion = '0.16.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +# patch needed for building h5py patches = ['unixccompiler-Python-2.7.11.patch'] # python needs bzip2 to build the bz2 package -- GitLab From 2d1318995610e78436b943b65f3a42f81f01bc2c Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 3 Mar 2016 18:12:35 +0100 Subject: [PATCH 0158/2403] fixed remarks --- .../freetype-2.6.2-CrayGNU-2015.11-XC.eb | 3 +- .../g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb | 24 +++++++++++ .../Python-2.7.11-CrayGNU-2015.11-XC.eb | 3 ++ .../SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb | 40 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb | 25 ++++++++++++ .../Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb | 26 ++++++++++++ 6 files changed, 120 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb index 97d02aea84..113ad0ada9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..9fa2e217a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb @@ -0,0 +1,24 @@ +# contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS=-mcmodel=large && ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 7eef88d995..5c7827f5c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -24,6 +24,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..f8f253cac7 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb new file mode 100644 index 0000000000..45169d651c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb new file mode 100644 index 0000000000..e34216f215 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 0a740288d25794de4b67b34db1a9f06d7f9ef89d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 4 Mar 2016 15:20:48 +0100 Subject: [PATCH 0159/2403] vcftools latest version --- ...CFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..fec3b7a05c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.14' + +homepage = 'https://vcftools.github.io/' +description = """A set of tools written in Perl and C++ for working with VCF files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/vcftools/vcftools/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl , perlver), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", + "vcf-fix-ploidy", "vcf-merge"]], + 'dirs': [], +} + +modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } + +moduleclass = 'bio' -- GitLab From 330716efb83e0e4a5cf01e160c121b8c1d333d37 Mon Sep 17 00:00:00 2001 From: perettig Date: Fri, 4 Mar 2016 17:52:06 +0100 Subject: [PATCH 0160/2403] removed tk (seems to break matplotlib) --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 5c7827f5c1..8b756292a1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -25,7 +25,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), ] -- GitLab From a833a112bf35362c1bfb476838dfbc4f6be6419d Mon Sep 17 00:00:00 2001 From: perettig Date: Sat, 5 Mar 2016 00:27:53 +0100 Subject: [PATCH 0161/2403] removed Tk version suffix to workaround matplotlib detection bug --- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 1 + ...ayGNU-2015.11-XC-no-X11.eb => Tk-8.6.4-CrayGNU-2015.11-XC.eb} | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb => Tk-8.6.4-CrayGNU-2015.11-XC.eb} (96%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 8b756292a1..45a3845e6a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -25,6 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), + ('Tk', '8.6.4'), ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb similarity index 96% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb index e34216f215..8aeedf1e3d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb @@ -2,7 +2,6 @@ easyblock = 'ConfigureMake' name = 'Tk' version = '8.6.4' -versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building -- GitLab From 3c765b249a4e0c23371b73296cbfd0952bad0153 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 17:38:21 +0100 Subject: [PATCH 0162/2403] moving Cray stuff to boost.py --- .../b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb index 5be4348909..9d5320a12a 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2015.11-XC-Python-2.7.11.eb @@ -1,5 +1,4 @@ # contributed by Luca Marsella (CSCS) -easyblock = 'boostcray' name = 'Boost' version = "1.60.0" -- GitLab From 1e3228ddbbea445c7ace7fc6272bbb89789b2fd3 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 19:35:13 +0100 Subject: [PATCH 0163/2403] GMP doesn't work with -02, using lowopt (-01) --- easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb index 9fa2e217a8..34e4ce0776 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb @@ -9,11 +9,12 @@ description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchainopts = {'lowopt': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] -preconfigopts = 'export CFLAGS=-mcmodel=large && ' +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' runtest = 'check' sanity_check_paths = { -- GitLab From d5a76df46e0f6394e6d77b3327d515e14048c818 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 7 Mar 2016 19:36:23 +0100 Subject: [PATCH 0164/2403] fixed remarks --- .../p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb index 45a3845e6a..8c373b7caf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb @@ -29,7 +29,7 @@ dependencies = [ ('GMP', '6.1.0'), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Mar 1st 2016 @@ -45,9 +45,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, - ], + 'patches': ['numpy-1.8.0-mkl.patch'], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], -- GitLab From d7616cf593103eb79f93c480e3e5e403d1b2e5f1 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 13:09:12 +0100 Subject: [PATCH 0165/2403] Add easyconfigs for SuperLU library --- .../c/CMake/CMake-3.2.3-ictce-7.3.5.eb | 31 +++++++++++++ .../s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 43 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb | 41 ++++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb new file mode 100644 index 0000000000..5ae7415b1c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb new file mode 100644 index 0000000000..7f7793d488 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'SuperLU' +version = '5.1.1' + +homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} + +source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] +sources = ["superlu_%(version)s.tar.gz"] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['260a3cd90b2100122abff38587a8290a'] + +# Set to ON to generate shared library +configopts = "-DBUILD_SHARED_LIBS=OFF" + +# Make sure not to build the slow BLAS library included in the package +configopts += " -Denable_blaslib=OFF" + +# Set the BLAS library to use +# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html +# Unfortunately, OpenBLAS is not recognized by FindBLAS from CMake, +# we have to specify the OpenBLAS library manually +configopts += ' -DBLAS_LIBRARIES="${EBROOTOPENBLAS}/lib/libopenblas.a;-pthread"' + +# Make symlink to version-numbered library filename +installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' + +builddependencies = [('CMake', '3.4.3')] +separate_build_dir = True + +runtest = "test" + +sanity_check_paths = { + 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb new file mode 100644 index 0000000000..514dd74cfa --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'SuperLU' +version = '5.1.1' + +homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'opt': True, 'pic': True} + +source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] +sources = ["superlu_%(version)s.tar.gz"] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['260a3cd90b2100122abff38587a8290a'] + +# Set to ON to generate shared library +configopts = "-DBUILD_SHARED_LIBS=OFF" + +# Make sure not to build the slow BLAS library included in the package +configopts += " -Denable_blaslib=OFF" + +# Set the BLAS library to use +# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html +configopts += " -DBLA_VENDOR=Intel10_64lp" + +# Make symlink to version-numbered library filename +installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' + +builddependencies = [('CMake', '3.2.3')] +separate_build_dir = True + +runtest = "test" + +sanity_check_paths = { + 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From 9e3cbd6e8dc553bf1e75d4f20feeeb581d22fca5 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 14:16:47 +0100 Subject: [PATCH 0166/2403] Correct filename --- .../{SuperLU-5.1.1-ictce-7.35.eb => SuperLU-5.1.1-ictce-7.3.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SuperLU/{SuperLU-5.1.1-ictce-7.35.eb => SuperLU-5.1.1-ictce-7.3.5.eb} (100%) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb similarity index 100% rename from easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.35.eb rename to easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb -- GitLab From b2e2dd698e6d46d333670b9ead5dad39b7eafe02 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 19:00:42 +0100 Subject: [PATCH 0167/2403] Simplify SuperLU easyconfigs to use the new easyblock --- .../s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 26 ------------------- .../s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 24 ----------------- 2 files changed, 50 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index 7f7793d488..d58d7f4d85 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'SuperLU' version = '5.1.1' @@ -7,7 +5,6 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] @@ -15,29 +12,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -# Set to ON to generate shared library -configopts = "-DBUILD_SHARED_LIBS=OFF" - -# Make sure not to build the slow BLAS library included in the package -configopts += " -Denable_blaslib=OFF" - -# Set the BLAS library to use -# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html -# Unfortunately, OpenBLAS is not recognized by FindBLAS from CMake, -# we have to specify the OpenBLAS library manually -configopts += ' -DBLAS_LIBRARIES="${EBROOTOPENBLAS}/lib/libopenblas.a;-pthread"' - -# Make symlink to version-numbered library filename -installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' - builddependencies = [('CMake', '3.4.3')] -separate_build_dir = True - -runtest = "test" - -sanity_check_paths = { - 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], - 'dirs': [], -} moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 514dd74cfa..4640b8c826 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'SuperLU' version = '5.1.1' @@ -7,7 +5,6 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} -toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] @@ -15,27 +12,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -# Set to ON to generate shared library -configopts = "-DBUILD_SHARED_LIBS=OFF" - -# Make sure not to build the slow BLAS library included in the package -configopts += " -Denable_blaslib=OFF" - -# Set the BLAS library to use -# cf https://cmake.org/cmake/help/latest/module/FindBLAS.html -configopts += " -DBLA_VENDOR=Intel10_64lp" - -# Make symlink to version-numbered library filename -installopts = ' && cd %(installdir)s/lib && ln -s libsuperlu_%(version)s.a libsuperlu.a' - builddependencies = [('CMake', '3.2.3')] -separate_build_dir = True - -runtest = "test" - -sanity_check_paths = { - 'files': ["include/supermatrix.h", "lib/libsuperlu.a"], - 'dirs': [], -} moduleclass = 'numlib' -- GitLab From 24b0a15e15d6580b506442a6c75e0e276c493fad Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Tue, 8 Mar 2016 22:06:15 +0100 Subject: [PATCH 0168/2403] Add toolchainopts --- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 1 + easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index d58d7f4d85..18ef21e40a 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -5,6 +5,7 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 4640b8c826..36729b6f64 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -5,6 +5,7 @@ homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'opt': True, 'pic': True} source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] sources = ["superlu_%(version)s.tar.gz"] -- GitLab From 7f7b81153e1f8356f2cc137617703c6e2d378afd Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Wed, 9 Mar 2016 11:44:05 +0100 Subject: [PATCH 0169/2403] Use CMake 3.4.3 for SuperLU-5.1.1-ictce-7.3.5 --- .../{CMake-3.2.3-ictce-7.3.5.eb => CMake-3.4.3-ictce-7.3.5.eb} | 2 +- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CMake/{CMake-3.2.3-ictce-7.3.5.eb => CMake-3.4.3-ictce-7.3.5.eb} (97%) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb similarity index 97% rename from easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 5ae7415b1c..7deb175b91 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'CMake' -version = '3.2.3' +version = '3.4.3' homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 36729b6f64..411ef70cfb 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -13,6 +13,6 @@ sources = ["superlu_%(version)s.tar.gz"] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['260a3cd90b2100122abff38587a8290a'] -builddependencies = [('CMake', '3.2.3')] +builddependencies = [('CMake', '3.4.3')] moduleclass = 'numlib' -- GitLab From 782e024dbab561cbe68d02bfd5d917f995130911 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Mar 2016 12:28:22 +0200 Subject: [PATCH 0170/2403] add easyconfig GDB-7.11-intel-2016a.eb --- .../easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb new file mode 100644 index 0000000000..fa5295e98e --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From 99d0f6d114d00a6526741abad4f07dbde9814973 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 13 Mar 2016 15:15:12 +0100 Subject: [PATCH 0171/2403] Update libint to 2016a and deps --- ....9.eb => Libint-2.0.5-intel-2016a-Python-2.7.11.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/Libint/{Libint-2.0.5-intel-2015a-Python-2.7.9.eb => Libint-2.0.5-intel-2016a-Python-2.7.11.eb} (74%) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb similarity index 74% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb index 91014bdb21..c56a331e40 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb @@ -1,24 +1,24 @@ name = 'Libint' version = '2.0.5' # Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 -versionsuffix = '-Python-2.7.9' +versionsuffix = '-Python-2.7.11' homepage = 'https://github.com/evaleev/libint' description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ - ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), - ('Boost', '1.57.0', versionsuffix), + ('GMP', '6.1.0'), + ('Boost', '1.60.0', versionsuffix), ] -builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150215')] # no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' -- GitLab From 3c1b969cc8fcdeb5b03f4fc67de55c4ec7164353 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 13 Mar 2016 15:16:19 +0100 Subject: [PATCH 0172/2403] Drop unused GMP --- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb deleted file mode 100644 index 70c2a1cb32..0000000000 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GMP' -version = '6.0.0a' - -homepage = 'http://gmplib.org/' -description = """GMP is a free library for arbitrary precision arithmetic, -operating on signed integers, rational numbers, and floating point numbers. """ - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'precise': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] - -# enable C++ interface -configopts = '--enable-cxx' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], - 'dirs': [], -} - -moduleclass = 'math' -- GitLab From b036c179c5d355f5ac43abfceaad55fd120fee2d Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 14 Mar 2016 11:16:38 +0100 Subject: [PATCH 0173/2403] removed -xc suffix --- ...-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11.eb} | 2 +- ...6.1.0-CrayGNU-2015.11-XC.eb => GMP-6.1.0-CrayGNU-2015.11.eb} | 2 +- ...1-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11.eb} | 2 +- ....11.eb => matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb} | 2 +- ...1-CrayGNU-2015.11-XC.eb => Python-2.7.11-CrayGNU-2015.11.eb} | 2 +- ....2-CrayGNU-2015.11-XC.eb => SQLite-3.9.2-CrayGNU-2015.11.eb} | 2 +- ...8.6.4-CrayGNU-2015.11-XC.eb => Tcl-8.6.4-CrayGNU-2015.11.eb} | 2 +- ...-8.6.4-CrayGNU-2015.11-XC.eb => Tk-8.6.4-CrayGNU-2015.11.eb} | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.6.2-CrayGNU-2015.11-XC.eb => freetype-2.6.2-CrayGNU-2015.11.eb} (92%) rename easybuild/easyconfigs/g/GMP/{GMP-6.1.0-CrayGNU-2015.11-XC.eb => GMP-6.1.0-CrayGNU-2015.11.eb} (91%) rename easybuild/easyconfigs/l/libpng/{libpng-1.6.21-CrayGNU-2015.11-XC.eb => libpng-1.6.21-CrayGNU-2015.11.eb} (92%) rename easybuild/easyconfigs/m/matplotlib/{matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb => matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb} (95%) rename easybuild/easyconfigs/p/Python/{Python-2.7.11-CrayGNU-2015.11-XC.eb => Python-2.7.11-CrayGNU-2015.11.eb} (98%) rename easybuild/easyconfigs/s/SQLite/{SQLite-3.9.2-CrayGNU-2015.11-XC.eb => SQLite-3.9.2-CrayGNU-2015.11.eb} (94%) rename easybuild/easyconfigs/t/Tcl/{Tcl-8.6.4-CrayGNU-2015.11-XC.eb => Tcl-8.6.4-CrayGNU-2015.11.eb} (91%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-CrayGNU-2015.11-XC.eb => Tk-8.6.4-CrayGNU-2015.11.eb} (91%) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb similarity index 92% rename from easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb index 113ad0ada9..7f9b603bc6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb index 34e4ce0776..6658db36ac 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb @@ -8,7 +8,7 @@ homepage = 'http://gmplib.org/' description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'lowopt': True} sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb similarity index 92% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb index bb061f924f..1b97f39104 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ version = '1.6.21' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb rename to easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb index 9a9609ca9e..7b58f1b605 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-XC-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """matplotlib is a python 2D plotting library which produces publi hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb similarity index 98% rename from easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 8c373b7caf..03be62fd52 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ version = "2.7.11" homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} numpyversion = '1.10.4' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb similarity index 94% rename from easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb index f8f253cac7..429cfc37d8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ version = '3.9.2' homepage = 'http://www.sqlite.org/' description = 'SQLite: SQL Database Engine in a C Library' -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} # eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz source_urls = ['http://www.sqlite.org/2015/'] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb index 45169d651c..0a0ed38e56 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.tcl.tk/' description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb similarity index 91% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb index 8aeedf1e3d..44900c63c7 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-XC.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.tcl.tk/' description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -- GitLab From 9c14105118bc6024193433750aff7ce1b43dc537 Mon Sep 17 00:00:00 2001 From: perettig Date: Mon, 14 Mar 2016 17:57:09 +0100 Subject: [PATCH 0174/2403] removed -XC suffix --- ....eb => h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb} | 2 +- ...al.eb => h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/h5py/{h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb => h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb} (94%) rename easybuild/easyconfigs/h/h5py/{h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb => h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb} (93%) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb similarity index 94% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb index 4422d5da72..c76da3b9b7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-parallel.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb @@ -8,7 +8,7 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb similarity index 93% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb index 131a99a851..728dc02b11 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-XC-Python-2.7.11-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb @@ -8,7 +8,7 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" -toolchain = {'name': 'CrayGNU', 'version': '2015.11-XC'} +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From d8bf857a307113e1541033bfc4af67cbef5a358f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 10:35:31 +0100 Subject: [PATCH 0175/2403] use HOME constant in new icc/ifort/imkl/impi easyconfigs --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 4 +--- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 4 +--- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 +-- 4 files changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 080cfccc9a..fad8d6d04d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 3ee926155e..16a589b7f3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,8 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 74cc4cff3a..dd75357fc5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,9 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index ef29e9af70..faa72cc81c 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,8 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + 'licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From d8b707a6e21dba177b222b93322c3798dd0677ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2016 13:09:20 +0100 Subject: [PATCH 0176/2403] add missing '/' --- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index fad8d6d04d..5c1c6d97c5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 16a589b7f3..5844c8abd9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index dd75357fc5..d1edf0b015 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['536dbd82896d6facc16de8f961d17d65'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index faa72cc81c..eaf9a3b7a7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['1c14656859d48bf8b90c71dace2a977b'] dontcreateinstalldir = 'True' -license_file = HOME + 'licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 9cb1e88ea4838c9df0b08239be240363570cdbce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 15 Mar 2016 16:47:53 +0100 Subject: [PATCH 0177/2403] added segemehl-0.2.0-goolf-1.4.10.eb --- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..39c950b357 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.2.0" + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """ segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] +sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] + +parallel = 1 + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From 879367d44a6c35a140b66f19552ca12bf4bcf09b Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 16 Mar 2016 14:00:40 +0100 Subject: [PATCH 0178/2403] RAxML 8.2.4-hybrid-avx2 for foss 2016a --- .../RAxML-8.2.4-foss-2016a-hybrid-avx2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb new file mode 100644 index 0000000000..431ef0ff1d --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.4' +versionsuffix ='-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-HYBRID-AVX2"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 90fa22472b6cfc099996ca3b9335d92339d1041e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:45:42 +0100 Subject: [PATCH 0179/2403] rainbow-2.0.4-goolf-1.4.10.eb --- .../r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..c431cc2a4f --- /dev/null +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'rainbow' +version = '2.0.4' + +homepage = 'https://sourceforge.net/projects/bio-rainbow/' +description = """Efficient tool for clustering and assembling short reads, especially for RAD.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://downloads.sourceforge.net/project/bio-rainbow/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +buildopts = ' CC=$CC' + +files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', + 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/rainbow', 'bin/ezmsim', 'bin/rbasm'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7e1d2ba87aabccafdc34a72438f79de067394201 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:47:49 +0100 Subject: [PATCH 0180/2403] PEAR-0.9.6-goolf-1.4.10.eb --- .../p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..5ee2eb89d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.6' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0e5d1dc188f3920467c8ddd6ff17c9fd7ac64b5c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 16 Mar 2016 18:50:52 +0100 Subject: [PATCH 0181/2403] Mawk-1.3.4-goolf-1.4.10-20150503.eb --- .../Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb new file mode 100644 index 0000000000..7235621e5d --- /dev/null +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'Mawk' +version = '1.3.4' +versionsuffix = '-20150503' + +homepage = 'http://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://invisible-island.net/mawk/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 887023130eadcc6a55f01d695d6cec31ef56a599 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 14:17:05 -0500 Subject: [PATCH 0182/2403] Adding an Easyconfig file for gtool-v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb new file mode 100644 index 0000000000..276283587b --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 02c80db3e5edf4c515e7c2e84cba772f41ed4867 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 16:55:18 -0500 Subject: [PATCH 0183/2403] Adding Easyconfig file for shapeit_v2.r837_GLIBCv2.12 --- ...shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb new file mode 100644 index 0000000000..a71ba8d96d --- /dev/null +++ b/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'shapeit' +version = '2.r837.GLIBCv2.12' +versionsuffix = '_linux_x86_64' + +homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' +description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] +sources = ['shapeit.v%(version)s.Linux.static.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["bin/shapeit", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 4ac34ac670957972ae454538b960cf7b2b57bd5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 17 Mar 2016 17:08:51 -0500 Subject: [PATCH 0184/2403] Adding author to the Easyconfig file for gtool --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 276283587b..aa280fb576 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -1,5 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: +# Author: Ravi Tripathi easyblock = "Binary" -- GitLab From b42b09ef2b1fdebe5b1d98891eed75169834e0f9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:12:56 -0500 Subject: [PATCH 0185/2403] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5-linux_x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb new file mode 100644 index 0000000000..aa280fb576 --- /dev/null +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi + +easyblock = "Binary" + +name = 'gtool' +version = '0.7.5' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' +description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] +sources = ['gtool_v%(version)s_x86_64.tgz'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["gtool", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' -- GitLab From 38474722b49c807cdbe36716e92088c8f989803d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:15:47 -0500 Subject: [PATCH 0186/2403] Changing the name of Easyconfig file for gtool v0.7.5 --- .../g/gtool/gtool-0.7.5_linux_x86_64.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb deleted file mode 100644 index aa280fb576..0000000000 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ /dev/null @@ -1,27 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi - -easyblock = "Binary" - -name = 'gtool' -version = '0.7.5' -versionsuffix = '_linux_x86_64' - -homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] -sources = ['gtool_v%(version)s_x86_64.tgz'] - -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - -sanity_check_paths = { - 'files': ["gtool", "LICENCE"], - 'dirs': ["example"] -} - -moduleclass = 'bio' -- GitLab From 9f51538585027769015932d76f80f27967b610f7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 18 Mar 2016 02:19:51 -0500 Subject: [PATCH 0187/2403] Change the name of easyconfig file for shapeit-v2.r837_GLIBCv2.12 --- ...linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb => shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit_v2.r837_GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb -- GitLab From f2ecb8a398d2a16aecb24c378131202077b6f485 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 20 Mar 2016 11:45:55 +0200 Subject: [PATCH 0188/2403] add easyconfig EasyBuild-2.7.0.eb --- .../e/EasyBuild/EasyBuild-2.7.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb new file mode 100644 index 0000000000..1ca29896e8 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.7.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 4dcdd9aa5726c945a7301332f00b431d1db3da86 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:30:39 +0100 Subject: [PATCH 0189/2403] add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb --- .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 10 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a07b7c3608e80cb5bbbcd8ad159231b462582047 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:39:44 +0100 Subject: [PATCH 0190/2403] add easyconfig libXext-1.3.3-foss-2016a.eb --- .../l/libXext/libXext-1.3.3-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..fc57003279 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From ada59b306cff8427daa61380d50f9e4419e1f6dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 08:56:07 +0100 Subject: [PATCH 0191/2403] add easyconfig libXft-2.3.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb --- .../fontconfig-2.11.94-foss-2016a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 22 +++++++++++++ .../l/libXft/libXft-2.3.2-foss-2016a.eb | 31 +++++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 28 +++++++++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++++ 5 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..41c2f0204e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb new file mode 100644 index 0000000000..1a968a5ada --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.2'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..eee347a314 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 61e73501ae42f1a56e50031555bd20d3cf4aeb0d Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 09:00:48 +0100 Subject: [PATCH 0192/2403] add easyconfig PCRE-8.38-foss-2016a.eb --- .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' -- GitLab From 9634929b1625d06d856861cb444495085dbe9659 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 21 Mar 2016 09:30:35 +0100 Subject: [PATCH 0193/2403] BayeScan/BayeScan-2.1-goolf-1.4.10.eb --- .../b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..664c8f53a4 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScan' +version = '2.1' + +homepage = 'http://cmpg.unibe.ch/software/BayeScan/' +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, + using differences in allele frequencies between populations.""" + +# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] +sources = ['%(name)s%(version)s.zip'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescan_%(version)s'], 'bin'), 'BayeScan%(version)s_manual.pdf' , 'input_examples', 'R functions'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescan_%(version)s'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 85471cb0716f38691dff6baf1aa00a73ba0845b8 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 17:49:48 +0100 Subject: [PATCH 0194/2403] add easyconfig gperf-3.0.4-foss-2016a.eb --- .../g/gperf/gperf-3.0.4-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..0547875020 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 1017f5824cdac5303667b828d4b0c54a1b5d73eb Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:10:54 +0100 Subject: [PATCH 0195/2403] modify easyconfig bzip2-1.0.6-foss-2016a.eb, add easyconfig gettext-0.19.6-foss-2016a.eb, add easyconfig GraphicsMagick-1.3.23-foss-2016a.eb, modify easyconfig libjpeg-turbo-1.4.2-foss-2016a.eb, add easyconfig LibTIFF-4.0.6-foss-2016a.eb, modify easyconfig libtool-2.4.6-foss-2016a.eb, modify easyconfig libxml2-2.9.3-foss-2016a.eb, add easyconfig XZ-5.2.2-foss-2016a.eb --- .../GraphicsMagick-1.3.23-foss-2016a.eb | 34 +++++++++++++++++++ .../g/gettext/gettext-0.19.6-foss-2016a.eb | 18 ++++++++++ .../l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 33 ++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 30 ++++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb new file mode 100644 index 0000000000..e3433e3f0b --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.23' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.3'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb new file mode 100644 index 0000000000..1fdb744032 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb new file mode 100644 index 0000000000..d7aa3b2df4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb new file mode 100644 index 0000000000..2a89ca6af6 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.6'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From e5236a98d2ea36fb4c3a4aa8ed4eb98f0f43f076 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:29:11 +0100 Subject: [PATCH 0196/2403] add easyconfig qrupdate-1.1.2-foss-2016a.eb --- .../q/qrupdate/qrupdate-1.1.2-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..27976f981b --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 994d6f447d81fb081150ce1a1aec518a4bd2d45b Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 18:40:00 +0100 Subject: [PATCH 0197/2403] add easyconfig HDF5-1.8.16-foss-2016a-serial.eb --- .../h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb new file mode 100644 index 0000000000..2936e9795e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 7a94c71bd384f3f1dc82777fc7abd5c24f5fcfab Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 20:51:41 +0100 Subject: [PATCH 0198/2403] add easyconfig GLib-2.47.5-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig libICE-1.0.9-foss-2016a.eb, add easyconfig libSM-1.2.2-foss-2016a.eb, add easyconfig libXt-1.1.5-foss-2016a.eb, add easyconfig Qt-4.8.7-foss-2016a.eb --- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 ++++++++++++++++ .../l/libICE/libICE-1.0.9-foss-2016a.eb | 27 +++++++++++++ .../l/libSM/libSM-1.2.2-foss-2016a.eb | 28 +++++++++++++ .../l/libXt/libXt-1.1.5-foss-2016a.eb | 39 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++ .../easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb | 24 ++++++++++++ 6 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..06841954c4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.6'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb new file mode 100644 index 0000000000..fa49f6c97c --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..fe3df1bbcf --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb new file mode 100644 index 0000000000..e37e36b1f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), +] + +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb new file mode 100644 index 0000000000..fd0d5932c9 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a.eb @@ -0,0 +1,24 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.47.5'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From 916e9d74d7e679b04d4ac0e44f1f3df12ca03d13 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:23:46 +0100 Subject: [PATCH 0199/2403] add easyconfig eudev-3.1.5-foss-2016a.eb, add easyconfig fixesproto-5.0-foss-2016a.eb, add easyconfig fontsproto-2.1.3-foss-2016a.eb, add easyconfig glproto-1.4.17-foss-2016a.eb, add easyconfig libdrm-2.4.67-foss-2016a.eb, add easyconfig libfontenc-1.1.3-foss-2016a.eb, add easyconfig libpciaccess-0.13.4-foss-2016a.eb, add easyconfig libXdamage-1.1.4-foss-2016a.eb, add easyconfig libXfixes-5.0.1-foss-2016a.eb, add easyconfig libXfont-1.5.1-foss-2016a.eb, add easyconfig makedepend-1.0.5-foss-2016a.eb, add easyconfig Mesa-11.1.2-foss-2016a.eb, add easyconfig pkg-config-0.29-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../e/eudev/eudev-3.1.5-foss-2016a.eb | 32 +++++++++ .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 ++++++ .../fontsproto/fontsproto-2.1.3-foss-2016a.eb | 20 ++++++ .../g/glproto/glproto-1.4.17-foss-2016a.eb | 20 ++++++ .../libXdamage/libXdamage-1.1.4-foss-2016a.eb | 25 +++++++ .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++ .../l/libXfont/libXfont-1.5.1-foss-2016a.eb | 31 +++++++++ .../l/libdrm/libdrm-2.4.67-foss-2016a.eb | 28 ++++++++ .../libfontenc/libfontenc-1.1.3-foss-2016a.eb | 23 +++++++ .../libpciaccess-0.13.4-foss-2016a.eb | 26 +++++++ .../m/Mesa/Mesa-11.1.2-foss-2016a.eb | 68 +++++++++++++++++++ .../makedepend/makedepend-1.0.5-foss-2016a.eb | 20 ++++++ .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 ++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 ++++++ 14 files changed, 385 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb new file mode 100644 index 0000000000..3265e4fdb4 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..4fe8f2b4dc --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb new file mode 100644 index 0000000000..0d7fd4a4a2 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'fontsproto' +version = '2.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X11 font extension wire protocol" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb new file mode 100644 index 0000000000..d26077ac1e --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb new file mode 100644 index 0000000000..19c75463d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.%s' % SHLIB_EXT, 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb new file mode 100644 index 0000000000..b62ce08a63 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', '2.6.2'), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb new file mode 100644 index 0000000000..93d87d9533 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.67-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.67' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..b21fd6654e --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfontenc' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/xlibs/' +description = """X11 font encoding library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.%s' % SHLIB_EXT, 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb new file mode 100644 index 0000000000..75924f159f --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('xorg-macros', '1.19.0'), +] + +preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c9dd66c1c1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.1.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.67'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1'), + ('LLVM', '3.7.1'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb new file mode 100644 index 0000000000..8bd95eee91 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 441307a0cbfd668e39a248b8a868d3edfa9e331c Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:28:31 +0100 Subject: [PATCH 0200/2403] add easyconfig GLPK-4.58-foss-2016a.eb --- .../g/GLPK/GLPK-4.58-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb new file mode 100644 index 0000000000..d5751eec2a --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.58' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 20a9dff4b702a113c5e9375b03ff2aeb68147707 Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:38:33 +0100 Subject: [PATCH 0201/2403] add easyconfig freeglut-3.0.0-foss-2016a.eb, add easyconfig GL2PS-1.3.9-foss-2016a.eb, add easyconfig libGLU-9.0.0-foss-2016a.eb, add easyconfig libXi-1.7.6-foss-2016a.eb, add easyconfig libXmu-1.1.2-foss-2016a.eb, add easyconfig libXpm-3.5.11-foss-2016a.eb, add easyconfig libXrandr-1.5.0-foss-2016a.eb, add easyconfig randrproto-1.5.0-foss-2016a.eb --- .../f/freeglut/freeglut-3.0.0-foss-2016a.eb | 37 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.3.9-foss-2016a.eb | 34 +++++++++++++++++ .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 ++++++++++++ .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++ .../l/libXmu/libXmu-1.1.2-foss-2016a.eb | 25 +++++++++++++ .../l/libXpm/libXpm-3.5.11-foss-2016a.eb | 22 +++++++++++ .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 ++++++++++++++++ .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 ++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb new file mode 100644 index 0000000000..aa4fa34ea2 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', '11.1.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb new file mode 100644 index 0000000000..f83060a449 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c219eeb168 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%%(name)s.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb new file mode 100644 index 0000000000..1cc567cb36 --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.6')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.%s' % SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..eab697bf89 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 40ee838e51bc76352a13168ef86058d8d4dfa8dc Mon Sep 17 00:00:00 2001 From: hajgato Date: Mon, 21 Mar 2016 22:53:41 +0100 Subject: [PATCH 0202/2403] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig gnuplot-5.0.3-foss-2016a.eb, add easyconfig GObject-Introspection-1.47.1-foss-2016a.eb, add easyconfig HarfBuzz-1.1.3-foss-2016a.eb, add easyconfig libcerf-1.4-foss-2016a.eb, add easyconfig libgd-2.1.1-foss-2016a.eb, add easyconfig Pango-1.39.0-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 49 +++++++++++++++++++ ...GObject-Introspection-1.47.1-foss-2016a.eb | 47 ++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.3-foss-2016a.eb | 42 ++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 34 +++++++++++++ .../l/libcerf/libcerf-1.4-foss-2016a.eb | 28 +++++++++++ .../l/libgd/libgd-2.1.1-foss-2016a.eb | 26 ++++++++++ .../p/Pango/Pango-1.39.0-foss-2016a.eb | 31 ++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 ++++++++ 8 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..3684c31e54 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +glibver = '2.47.5' + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] +builddependencies = [ + ('renderproto', '0.11'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb new file mode 100644 index 0000000000..3c83530c29 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.47.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +pyver = '2.7.11' + +dependencies = [ + ('Python', pyver), + ('GLib', '2.47.5'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), + ('libffi', '3.2.1'), +] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb new file mode 100644 index 0000000000..7e42e00e67 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.3' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('libgd', '2.1.1'), + ('Pango', '1.39.0'), + ('libcerf', '1.4'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..91db4cfacd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.1.3' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('freetype', '2.6.2'), + ('GObject-Introspection', '1.47.1') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb new file mode 100644 index 0000000000..4f3471b4f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.4-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.4' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..b645a00595 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.1.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.1.1' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/libgd/gd-libgd/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.11.94'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb new file mode 100644 index 0000000000..80529d5bda --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.39.0' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.47.5' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.1.3'), + ('GObject-Introspection', '1.47.1'), + ('fontconfig', '2.11.94') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 10ce3ec28443fcbb03da191301541162aa2ad8b7 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 10:10:33 +0100 Subject: [PATCH 0203/2403] OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb --- .../OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..37166d7311 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,59 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +name = "OpenMM" +version = "6.1" + +easyblock = "CMakeMake" + +homepage = 'https://simtk.org/home/openmm' +description = """OpenMM is a toolkit for molecular simulation.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +source_urls = ['https://github.com/pandegroup/openmm/archive/'] +sources = ['%(version)s.tar.gz'] + +parallel = 1 + +builddependencies = [ + ('CMake', '2.8.12'), +] + +separate_build_dir = True + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SWIG', '2.0.4', '-Python-2.7.5'), +] + +runtest = ' test' + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["lib/libOpenMM.so", "lib/python%s/site-packages/simtk/openmm/openmm.py" % (pyshortver)], + 'dirs': [] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%s/site-packages' % (pyshortver), +} + +modextravars = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' -- GitLab From 09f2c97bc278a4a2ea87de7137f1a2234a539801 Mon Sep 17 00:00:00 2001 From: hajgato Date: Tue, 22 Mar 2016 10:26:15 +0100 Subject: [PATCH 0204/2403] add easyconfig FLTK-1.3.3-foss-2016a.eb, add easyconfig libXcursor-1.1.14-foss-2016a.eb, add easyconfig libXinerama-1.1.3-foss-2016a.eb, add easyconfig xineramaproto-1.2.1-foss-2016a.eb, add easyconfig xprop-1.2.2-foss-2016a.eb --- .../f/FLTK/FLTK-1.3.3-foss-2016a.eb | 37 +++++++++++++++++++ .../libXcursor-1.1.14-foss-2016a.eb | 29 +++++++++++++++ .../libXinerama-1.1.3-foss-2016a.eb | 31 ++++++++++++++++ .../xineramaproto-1.2.1-foss-2016a.eb | 19 ++++++++++ .../x/xprop/xprop-1.2.2-foss-2016a.eb | 26 +++++++++++++ 5 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..650bf33743 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -0,0 +1,37 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + + +dependencies = [ + ('libX11', '1.6.3'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2'), + ('xprop', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid'], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb new file mode 100644 index 0000000000..1fc949ad4e --- /dev/null +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXcursor' +version = '1.1.14' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Cursor management library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXfixes', '5.0.1'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xcursor/Xcursor.h', 'lib/libXcursor.%s' % SHLIB_EXT, 'lib/libXcursor.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..e0a2e3d206 --- /dev/null +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXinerama' +version = '1.1.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Xinerama multiple monitor library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('xineramaproto', '1.2.1'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXinerama.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a40280e419 --- /dev/null +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xineramaproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/panoramiXproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb new file mode 100644 index 0000000000..bd60b7c873 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('xorg-macros', '1.19.0'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6ccd02bdb1d7397de31d2b3f8060e559b373798e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 22 Mar 2016 11:29:53 +0100 Subject: [PATCH 0205/2403] Update GraphicsMagick-1.3.23-foss-2016a.eb -fpic needed by Octacve --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index e3433e3f0b..6fa3747197 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From 803e8384f663f340a66fa4ea79d36fc448b63b3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Mar 2016 11:32:09 +0100 Subject: [PATCH 0206/2403] Octave needs pic --- .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index 755ecbe16c..ea37c3e81c 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -7,6 +7,7 @@ homepage = 'http://www.graphicsmagick.org/' description = """GraphicsMagick is the swiss army knife of image processing.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ SOURCEFORGE_SOURCE, -- GitLab From e8b93739a75d8c20e97ab89028bb9b58fb7cf0cf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 11:53:27 +0100 Subject: [PATCH 0207/2403] BayeScEnv-1.1-goolf-1.4.10.eb --- .../b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7a976185d2 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScEnv' +version = '1.1' + +homepage = 'https://github.com/devillemereuil/bayescenv' +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/devillemereuil/bayescenv/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescenv'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 620bbf6dd938b5325c24e02d890e19c1383dae0f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 22 Mar 2016 11:55:29 +0100 Subject: [PATCH 0208/2403] added dependency SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb --- .../SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..55068068d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.4-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '2.0.4' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with +a variety of high-level programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [('http://sourceforge.net/projects/swig/files/swig/swig-%s/' % version, 'download')] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.12'), +] + +moduleclass = 'devel' -- GitLab From 46c14aa7795447b96c6714043a15b2a03210f153 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Mar 2016 12:09:24 +0100 Subject: [PATCH 0209/2403] {math}[foss-2016a] Octave 4.0.0 (REVIEW) --- .../a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb | 25 ++++++++ .../o/Octave/Octave-4.0.0-foss-2016a.eb | 58 +++++++++++++++++++ .../q/Qhull/Qhull-2015.2-foss-2016a.eb | 37 ++++++++++++ ...uiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb | 24 ++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb new file mode 100644 index 0000000000..939e49dbc0 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.3.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb new file mode 100644 index 0000000000..bf4776d474 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.0.0' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXft', '2.3.2'), + ('PCRE', '8.38'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.3.0'), + ('cURL', '7.47.0'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLPK', '4.58'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.3'), + ('Java', '1.8.0_72', '', True), + ('zlib', '1.2.8'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt', '4.8.7'), + ('HDF5', '1.8.16', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.1', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.23'), +] + +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb new file mode 100644 index 0000000000..c145ad7bf0 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt +# and https://github.com/Homebrew/homebrew-science/issues/3353 +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..7b07d451fc --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.1' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'LAPACK="$LIBLAPACK" ' +prebuildopts = 'LAPACK="$LIBLAPACK" ' +preinstallopts = 'LAPACK="$LIBLAPACK" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 1527993f12857255edb7ffbd9efcf6da5fd95aee Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 22 Mar 2016 21:47:20 +0000 Subject: [PATCH 0210/2403] Update rtracklayer to 1.30.3 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index d1392d23cc..78a36e128c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 60d39797ec..42093e636a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.2', bioconductor_options), + ('rtracklayer', '1.30.3', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From d2f49d06ce3607de57e4bb93705bde9247dfdd3e Mon Sep 17 00:00:00 2001 From: fenoyc Date: Thu, 24 Mar 2016 14:25:31 +0100 Subject: [PATCH 0211/2403] add easyconfig OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb --- .../OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..456a180ae7 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.2-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' -- GitLab From 95827494b4f314243b046063bd45bbc3eafc50f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Mar 2016 16:32:58 +0200 Subject: [PATCH 0212/2403] modify easyconfig GCCcore-4.9.3.eb --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index 268b052687..78428e12c5 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -25,7 +25,10 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] -- GitLab From af28806336f567e64466ba8f29d19006bfd9612a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 17:58:21 +0200 Subject: [PATCH 0213/2403] add easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb new file mode 100644 index 0000000000..eed56a9078 --- /dev/null +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Saxon-HE' +version = '9.7.0.4' + +homepage = 'http://saxon.sourceforge.net' +description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] + +source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] + +versionsuffix = '-Java-%(javaver)s' + +dependencies = [('Java', '1.7.0_79')] + +jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] + +sanity_check_paths = { + 'files': jarfiles, + 'dirs': [], +} + +modextrapaths = {'CLASSPATH': jarfiles} + +moduleclass = 'devel' -- GitLab From cca33c128a3ac475714f4c99fea45fb369affbb2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Mar 2016 18:18:48 +0200 Subject: [PATCH 0214/2403] modify easyconfig M4-1.4.17-GCCcore-4.9.3.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index c1c8a52948..02f06d5cfe 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 73a8f1353ac0011e1c698eee8587510a306c8898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 24 Mar 2016 17:24:33 +0100 Subject: [PATCH 0215/2403] Bump FSL to intel/2016a --- .../f/FSL/FSL-5.0.9-intel-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb new file mode 100644 index 0000000000..145ff09b91 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'FSL' +version = '5.0.9' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0'), + ('expat', '2.1.0'), + ('libX11', '1.6.3'), +] + +moduleclass = 'bio' -- GitLab From 4f63d5fd457e914b17b505a79ab9b948dac38ef5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:42:15 +0200 Subject: [PATCH 0216/2403] modify easyconfig Tk-8.6.4-foss-2016a-no-X11.eb --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb index 6f98f7076c..449ce63a29 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8') ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From 7d31e07e4d50572096fe299846f23480ab5f8264 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 08:50:57 +0200 Subject: [PATCH 0217/2403] modify easyconfig M4-1.4.17-foss-2016a.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index 0d030e3264..ce563e7def 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 123ca05e26b955947108f4f3a2bb414138e46df9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 10:40:25 +0200 Subject: [PATCH 0218/2403] add easyconfig ant-1.9.6-Java-1.7.0_79.eb --- .../a/ant/ant-1.9.6-Java-1.7.0_79.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb new file mode 100644 index 0000000000..3ee7c5b406 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -0,0 +1,23 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.7.0_79')] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9bcdda139d149aac176a17a5aa9f38b137e55d83 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 25 Mar 2016 13:48:00 +0000 Subject: [PATCH 0219/2403] Update Bowtie2 to 2.2.8 for recent foss --- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 40 +++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb new file mode 100644 index 0000000000..29bf068b6a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb new file mode 100644 index 0000000000..e48888855e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.8' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 9f4fb4098262af3f3388b25be24f4eeb890274b2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:17:01 +0200 Subject: [PATCH 0220/2403] add easyconfig Blitz++-0.10-foss-2016a.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb new file mode 100644 index 0000000000..03886c8db9 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', + 'download'] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', + 'include/blitz/gnu', + 'include/blitz/meta', + 'include/random', + 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 020f92e1035043d6dbfcc9e9e7bfe2a80e9f9aa0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 0221/2403] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../fontconfig-2.11.94-foss-2016a.eb | 22 ++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 21 ++++++++++++++ .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 4 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb new file mode 100644 index 0000000000..d955835431 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.94' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6.2'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb new file mode 100644 index 0000000000..3111a314be --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1d95e0d44afa8bd2a6d3dd12f779f03f377eab75 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:22:11 +0200 Subject: [PATCH 0222/2403] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From a429536dc79733a15a2ecdbf335fcbed1f2990df Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:24:03 +0200 Subject: [PATCH 0223/2403] add easyconfig MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..a11de24d4f --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.11'), + ('HDF5', '1.8.16'), + ('libxml2', '2.9.3', '-Python-%(pyver)s') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +buildopts = '-j 1' + +moduleclass = 'data' -- GitLab From 0f7f918444396849cefb3ddd10ec622ceb292c8a Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:42:38 -0500 Subject: [PATCH 0224/2403] Adding Email to the easyconfig --- easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb index aa280fb576..6d1dad133e 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 7665efa01e6c846d6fcc6299b62552125d23d5de Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 13:45:45 -0500 Subject: [PATCH 0225/2403] Adding email to shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb Easyconfig file --- .../s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb index a71ba8d96d..7441bd58af 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Ravi Tripathi +# Email: ravi89@uab.edu easyblock = "Binary" -- GitLab From 4bc1fe85404268c258d800beb130fe6597928b40 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 28 Mar 2016 14:07:21 -0500 Subject: [PATCH 0226/2403] Adding an Easyconfig file for MRICron built on 06/22/2015 --- .../m/mricron/mricron-062215-linux_x86_64.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb new file mode 100644 index 0000000000..a7fb738545 --- /dev/null +++ b/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Binary" + +name = 'mricron' +version = '062215' +versionsuffix = '_linux_x86_64' + +homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' +description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] +sources = ['lx.zip'] + +# Following commands are used to untar the file and copy the content to install directory +install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +install_cmd += "cp -a %(builddir)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], + 'dirs': ["example", "lut", "templates"] +} + +moduleclass = 'bio' -- GitLab From cff82a7a7cce953ae7c746a6227a1e01777bf81f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:40:39 +0100 Subject: [PATCH 0227/2403] Use latest numpy and fix tests --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b.eb | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb index c0f1f917f6..c33eb72992 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb @@ -1,3 +1,7 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + easyblock = 'PythonPackage' name = 'RSeQC' @@ -16,20 +20,22 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -patches = [] - -Python = 'Python' +python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), - ('numpy', '1.9.2'), + ('numpy', '1.10.1', versionsuffix), ] +runtest = "python setup.py test" + sanity_check_paths = { 'files': [], - 'dirs': ["."] + 'dirs': ["bin", "lib"] } +options = {'modulename': 'qcmodule'} + moduleclass = 'bio' -- GitLab From 9403a1c1ed2e243ded00fd181b7c3e74f6f8061c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 28 Mar 2016 23:48:28 +0100 Subject: [PATCH 0228/2403] Remove obsolete numpy dep for RSeQC --- .../numpy-1.9.2-foss-2015b-Python-2.7.10.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb deleted file mode 100644 index f55df325cf..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-foss-2015b-Python-2.7.10.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'numpy' -version = '1.9.2' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2015b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = ['numpy-1.8.0-mkl.patch'] - -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('SuiteSparse', '4.4.5', '-METIS-5.1.0'), -] - -moduleclass = 'math' -- GitLab From bda5cb872c43f93c6f7207cdf42e96364661b7a0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:45:09 +0100 Subject: [PATCH 0229/2403] Add BEDTools 2.25.0 to foss-2015b and foss-2016a --- .../b/BEDTools/BEDTools-2.25.0-foss-2015b.eb | 33 +++++++++++++++++++ .../b/BEDTools/BEDTools-2.25.0-foss-2016a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb new file mode 100644 index 0000000000..50f76cdae7 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb new file mode 100644 index 0000000000..89147e0b20 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.25.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 9e31cc2f81179ae76942ac50899220609c8d5438 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 07:59:12 +0100 Subject: [PATCH 0230/2403] Fix version, description, sanity check and build options --- .../s/Subread/Subread-1.5.0p1-foss-2015b.eb | 28 +++++++++---------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb index 245a7b2f5a..4fd69f051e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb @@ -1,30 +1,28 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# It was auto-generated based on a template easyconfig, so it should be used with care. +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute easyblock = 'MakeCp' name = 'Subread' -version = '1.5.0p1' +version = '1.5.0-p1' homepage = 'http://subread.sourceforge.net/' -description = """TEMPLATE DESCRIPTION""" +description = """High performance read alignment, quantification and mutation discovery""" -# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... -# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ -sources = ['%(namelower)s-%version)s-source.tar.gz'] -source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -patches = [] +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -dependencies = [] -# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] } moduleclass = 'bio' -- GitLab From 4b1b8e1b10c5d5378efc01381b9deb998f20c8f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 29 Mar 2016 08:02:18 +0100 Subject: [PATCH 0231/2403] Add foss-2016a port of Subread --- .../s/Subread/Subread-1.5.0p1-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb new file mode 100644 index 0000000000..1312eb0648 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0-p1' + +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] + +prebuildopts = 'cd src;' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] + + +sanity_check_paths = { + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] +} + +moduleclass = 'bio' -- GitLab From a64db51afb19dbd910faa66e8d84b4d7c4239e0b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 29 Mar 2016 10:19:18 +0200 Subject: [PATCH 0232/2403] Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb --- .../Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..47cae92462 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.9.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': False, 'pic': False} + +parallel = 1 + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), + ('cURL', '7.29.0'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.23.4', { + 'source_urls': ['http://cython.org/release/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] +} + +moduleclass = 'bio' -- GitLab From 31ee1fa4cc65d4d311b091272768ca615aa67949 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 29 Mar 2016 10:21:36 +0200 Subject: [PATCH 0233/2403] Revert "Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb" This reverts commit a64db51afb19dbd910faa66e8d84b4d7c4239e0b. --- .../Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100644 index 47cae92462..0000000000 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,55 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'Bundle' - -name = 'Pysam' -version = '0.9.0' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': False, 'pic': False} - -parallel = 1 - -python = 'Python' -pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('ncurses', '5.9'), - ('zlib', '1.2.8'), - ('cURL', '7.29.0'), -] - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - -exts_list = [ - ('Cython', '0.23.4', { - 'source_urls': ['http://cython.org/release/'], - }), - ('pysam', version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], - }), -] - -modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver], -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] -} - -moduleclass = 'bio' -- GitLab From 8466e1b77b8a8c23b3a659045371f9db70b304f4 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:02:06 +0200 Subject: [PATCH 0234/2403] New `.eb` files for LinBox 1.4.0, FFLAS-FFPACK 2.2.0, and Givaro 4.0.1 --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 70 +++++++++++++++++++ .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 45 ++++++++++++ .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 70 +++++++++++++++++++ 3 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..382acef001 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.2.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v2.2.0.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270041, + "build_time": 30.84, + "install_size": 1762928, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb new file mode 100644 index 0000000000..56ed27ad72 --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.0.1' + +homepage = 'http://givaro.forge.imag.fr/' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v4.0.1.zip'] +source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb new file mode 100644 index 0000000000..042673b61a --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.4.0' + +homepage = 'http://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'version': '2016a', 'name': 'foss'} + +sources = ['v1.4.0.zip'] +source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] + +builddependencies = [ + ('Autoconf', '2.69', '', True), + ('Automake', '1.15', '', True), + ('libtool', '2.4.6', '', True), +] +dependencies = [ + ('FFLAS-FFPACK', '2.2.0'), + ('Givaro', '4.0.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" + +parallel = 4 + +unwanted_env_vars = {} +start_dir = '%(builddir)s/%(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0dev0", + "easybuild-easyblocks_version": "2.8.0dev0", + "timestamp": 1459270157, + "build_time": 64.4, + "install_size": 8769443, + "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), + "core_count": 4, + "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", + "cpu_speed": 2400.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", + "glibc_version": "2.21", + "hostname": "xenia", + "os_name": "ubuntu", + "os_type": "Linux", + "os_version": "15.10", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", + "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", + "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", +}] -- GitLab From 842135094fa8af11889df5460b3aa58906661c11 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Tue, 29 Mar 2016 22:33:16 +0200 Subject: [PATCH 0235/2403] Remove "buildstatistics" section that sneaked in --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ------------------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 24 ------------------- 2 files changed, 48 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 382acef001..153536ed7b 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270041, - "build_time": 30.84, - "install_size": 1762928, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'FFLAS-FFPACK-2.2.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 042673b61a..df00b437d1 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -44,27 +44,3 @@ sanity_check_paths = { } moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0dev0", - "easybuild-easyblocks_version": "2.8.0dev0", - "timestamp": 1459270157, - "build_time": 64.4, - "install_size": 8769443, - "command_line": ['--add-dummy-to-minimal-toolchains', '--buildpath=/tmp', '--experimental', '--github-user=riccardomurri', '--installpath=/home/rmurri/w/easybuild', '--minimal-toolchains', '--module-syntax=Lua', '--modules-tool=Lmod', '--packagepath=/home/rmurri/w/easybuild/packages', '--prefix=/home/rmurri/w/easybuild', '--repositorypath=ebfiles', '--robot=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--robot-paths=/home/rmurri/w/easybuild/ebfiles:/home/rmurri/w/easybuild/easyconfigs/easybuild/easyconfigs/', '--skip-test-cases', '--sourcepath=/home/rmurri/w/easybuild/sources', '--try-toolchain="[\'foss\', \'2016a\']"', 'LinBox-1.4.0-foss-2015a.eb'], - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '5.8'), - "core_count": 4, - "cpu_model": "Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz", - "cpu_speed": 2400.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/home/rmurri/w/easybuild/software/GCCcore/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3 --with-local-prefix=/home/rmurri/w/easybuild/software/GCCcore/4.9.3; Thread model: posix; gcc version 4.9.3 (GCC) ; ", - "glibc_version": "2.21", - "hostname": "xenia", - "os_name": "ubuntu", - "os_type": "Linux", - "os_version": "15.10", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.10 (default, Oct 14 2015, 16:09:02) ; [GCC 5.2.1 20151010]", - "system_gcc_path": "/home/rmurri/w/easybuild/software/GCCcore/4.9.3/bin/gcc", - "system_python_path": "/home/rmurri/.virtualenvs/easybuild/bin/python", -}] -- GitLab From 1f0c0f48cdee7708fbcbbd1584e5539528823e2f Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Tue, 29 Mar 2016 15:42:59 -0700 Subject: [PATCH 0236/2403] add Nvidia OptiX 3.8.0 easyconfig --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..db096d2117 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' +name = 'OptiX' +version = '3.8.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] + +checksums = [ + 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'dirs': [] +} + +modextravars = { 'OPTIX_HOME': '%(installdir)s' } + +moduleclass = 'vis' -- GitLab From a192c8e8addf0c4d566a728cca056b438cc1e3fb Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 10:41:23 +0200 Subject: [PATCH 0237/2403] Edits suggested by @boegel and general cleanup. Some cruft was added by EB as a result of saving back the file, and it gets dutifully removed now. (Well, hopefully!) --- .../FFLAS-FFPACK-2.2.0-foss-2016a.eb | 24 ++++++++----------- .../g/Givaro/Givaro-4.0.1-foss-2016a.eb | 21 +++++++--------- .../l/LinBox/LinBox-1.4.0-foss-2016a.eb | 21 +++++++--------- 3 files changed, 26 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 153536ed7b..282843bbc7 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -17,30 +17,26 @@ description = "Finite Field Linear Algebra Subroutines / Package" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v2.2.0.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' - -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' +configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' + ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 56ed27ad72..fe391b51b5 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -17,29 +17,24 @@ description = "C++ library for arithmetic and algebraic computations" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v4.0.1.zip'] -source_urls = ['https://github.com/linbox-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ - ('GMP', '6.1.0', '', ('GCC', '4.9.3-2.25')), + ('GMP', '6.1.0'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-gmp=$EBROOTGMP --enable-inline" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index df00b437d1..4d00ba2bf0 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -17,30 +17,25 @@ description = "C++ library for exact, high-performance linear algebra" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v1.4.0.zip'] -source_urls = ['https://github.com/%(namelower)s-team/%(namelower)s/archive'] +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69', '', True), - ('Automake', '1.15', '', True), - ('libtool', '2.4.6', '', True), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.6'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFPACK --enable-openmp" -parallel = 4 - -unwanted_env_vars = {} -start_dir = '%(builddir)s/%(namelower)s-%(version)s/' - sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s/%(namelower)s-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From e0e12f2bcce4f121fbc00a1d3787a62d35c8766e Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 11:00:47 +0200 Subject: [PATCH 0238/2403] Use `Autotools` bundle instead of depending on each tool separately. --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 4 +--- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 4 +--- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 282843bbc7..94cd13bd81 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index fe391b51b5..4f0fbad866 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/givaro/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('GMP', '6.1.0'), diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 4d00ba2bf0..640a495db8 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -21,9 +21,7 @@ sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/linbox/archive'] builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.6'), + ('Autotools', '20150215'), ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), -- GitLab From 236a8879552482ac855d3c1fbbf69c0089fb53d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:47:31 +0200 Subject: [PATCH 0239/2403] {lang}[intel/2016a] numba 0.24.0 w/ Python 2.7.11 & 3.5.1 --- .../llvmlite-0.9.0_fix-ffi-Makefile.patch | 29 +++++++++++++ .../numba-0.24.0-intel-2016a-Python-2.7.11.eb | 41 +++++++++++++++++++ .../numba-0.24.0-intel-2016a-Python-3.5.1.eb | 41 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch new file mode 100644 index 0000000000..7a74cc0623 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.9.0_fix-ffi-Makefile.patch @@ -0,0 +1,29 @@ +don't use -static-libstdc++, causing problems like "glibc detected *** python: free(): invalid pointer" +cfr. https://github.com/numba/llvmlite/issues/93; +don't hardcode -lLLVMOProfileJIT, not required anymore +cfr. https://github.com/numba/llvmlite/issues/121 +author: Kenneth Hoste (HPC-UGent) +--- llvmlite-0.9.0/ffi/Makefile.linux.orig 2016-01-26 15:11:43.000000000 +0100 ++++ llvmlite-0.9.0/ffi/Makefile.linux 2016-03-30 12:41:34.102307156 +0200 +@@ -4,9 +4,7 @@ + # -flto and --exclude-libs allow us to remove those parts of LLVM we don't use + CXXFLAGS = $(LLVM_CXXFLAGS) -flto + LDFLAGS = $(LLVM_LDFLAGS) -flto -Wl,--exclude-libs=ALL +-# Need to add LLVMOProfileJIT by hand +-# see https://llvm.org/bugs/show_bug.cgi?id=25091 +-LIBS = $(LLVM_LIBS) -lLLVMOProfileJIT ++LIBS = $(LLVM_LIBS) + SRC = assembly.cpp bitcode.cpp core.cpp initfini.cpp module.cpp value.cpp \ + executionengine.cpp transforms.cpp passmanagers.cpp targets.cpp dylib.cpp \ + linker.cpp +@@ -15,9 +13,7 @@ + all: $(OUTPUT) + + $(OUTPUT): $(SRC) +- # static-libstdc++ avoids runtime dependencies on a +- # particular libstdc++ version. +- $(CXX) -static-libstdc++ -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) ++ $(CXX) -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) + + clean: + rm -rf test diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0ddf57da7d --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..e0e36eeb79 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From a45e7509603391b8a42eb3f1d333cfd902bfefc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 12:53:43 +0200 Subject: [PATCH 0240/2403] use right patch file for llvmlite --- .../n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb | 2 +- .../n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb index 0ddf57da7d..1ed8278597 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], diff --git a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb index e0e36eeb79..c11e1bdb17 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.24.0-intel-2016a-Python-3.5.1.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('llvmlite', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], - 'patches': ['llvmlite-0.8.0_no-static-libstc++.patch'], + 'patches': ['llvmlite-0.9.0_fix-ffi-Makefile.patch'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], -- GitLab From d54f8ea4ed5a925fb10a5f45ed6b6a9c2a5a5ec9 Mon Sep 17 00:00:00 2001 From: Giovanni Date: Wed, 30 Mar 2016 13:22:28 +0200 Subject: [PATCH 0241/2403] Added DCA++ bundle file for building the Dynamical Cluster Approximation software. The necessary easyconfig files where added, notably magma-2.0.0 and its patch file for linking to libcusparse. --- .../c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb | 24 ++++ .../d/DCA/DCA++-CMake-CrayGNU-2015.11.eb | 25 +++++ .../g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb | 45 ++++++++ .../m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 30 +++++ .../easyconfigs/m/magma/magma-2.0.0.patch | 106 ++++++++++++++++++ 5 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.0.0.patch diff --git a/easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..0fd1f3f091 --- /dev/null +++ b/easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +# Built with EasyBuild version 2.5.0 on 2016-01-22_09-06-09 +easyblock = 'ConfigureMake' + +name = 'CMake' +version = "3.3.1" + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file diff --git a/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb b/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..a03ec7b4ae --- /dev/null +++ b/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'DCA++' +version = '1.0' + +#consider building everything with eb: +#preinstallopts: change build_directory +#disable clean build directory + +homepage = 'http://www.itp.phys.ethz.ch/people/schulthess' +description = """This modules bundles all the dependencies for DCA++, the best DCA ever""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +dependencies = [ + ('CMake', '3.3.1'), + ('spglib', '1.7.3'), + ('NFFT', '3.3.0'), + ('magma', '2.0.0'), + ('gtest', '1.7.0'), + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..0942442516 --- /dev/null +++ b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb @@ -0,0 +1,45 @@ +# Built with EasyBuild version 2.5.0 on 2016-01-22_09-08-42 +easyblock = "Tarball" + +name = 'gtest' +version = '1.7.0' + +homepage = 'https://code.google.com/p/googletest/' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCE_ZIP] +source_urls = ['https://googletest.googlecode.com/files'] + +sanity_check_paths={ + 'files': ['CMakeLists.txt', ], + 'dirs': ['include', 'src'], +} + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.5.0", + "easybuild-easyblocks_version": "2.5.0", + "timestamp": 1453450122, + "build_time": 3.29, + "install_size": 5091756, + "command_line": ['--buildpath=/dev/shm/haehneru', '--experimental', '--external-modules-metadata=cray-netcdf/4.3.2,cray-hdf5/1.8.13,cray-hdf5-parallel/1.8.13,cray-libsci/13.0.4,cray-libsci/13.2.0,cudatoolkit/6.5.14-1.0502.9613.6.1,cudatoolkit/6.5.14-1.0502.9836.8.1,cudatoolkit/7.0.28-1.0502.10742.5.1,cray-petsc-complex-64/3.5.3.1,cray-petsc-complex/3.5.3.1,cray-petsc/3.5.3.1,cray-petsc-64/3.5.3.1,gcc/4.9.2', '--group-writable-installdir', '--hide-deps=Bison,Doxygen,JasPer,NASM,SQLite,Szip,Tcl,bzip2,cURL,flex,freetype,libjpeg-turbo,libpng,libreadline,libtool,libxml2,ncurses,zlib,M4,Serf,APR,APR-util,expat,SCons', '--installpath=/project/s299/easybuild/daint/easybuild', '--optarch=sandybridge', '--packagepath=/project/s299/easybuild/daint/easybuild/packages', '--prefix=/project/s299/easybuild/daint/easybuild', '--repositorypath=/project/s299/easybuild/daint/easybuild/ebfiles_repo/', '--robot=/apps/common/easybuild/cscs_easyconfigs/:/apps/common/easybuild/ebfiles_repo/daint:/apps/common/UES/easybuild/software/EasyBuild/2.5.0/lib64/python2.6/site-packages/easybuild_easyconfigs-2.5.0-py2.6.egg/easybuild/easyconfigs', '--robot-paths=/apps/common/easybuild/cscs_easyconfigs/:/apps/common/easybuild/ebfiles_repo/daint:', '--set-gid-bit', '--sourcepath=/users/haehneru', '--umask=002', 'DCA++-CMake-CrayGNU-2015.06-XC.eb'], + "modules_tool": ('EnvironmentModulesC', '/opt/modules/3.2.10.3/bin/modulecmd', '3.2.10'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2599.904, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/opt/gcc/4.8.2/bin/../snos/bin/gcc; COLLECT_LTO_WRAPPER=/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/lto-wrapper; Target: x86_64-suse-linux; Configured with: ../cray-gcc-4.8.2/configure --prefix=/opt/gcc/4.8.2/snos --disable-nls --libdir=/opt/gcc/4.8.2/snos/lib --enable-languages=c,c++,fortran --with-gxx-include-dir=/opt/gcc/4.8.2/snos/include/g++ --with-slibdir=/opt/gcc/4.8.2/snos/lib --with-system-zlib --enable-shared --enable-__cxa_atexit --build=x86_64-suse-linux --with-mpc=/opt/gcc/mpc/0.8.1 --with-mpfr=/opt/gcc/mpfr/2.4.2 --with-gmp=/opt/gcc/gmp/4.3.2; Thread model: posix; gcc version 4.8.2 20131016 (Cray Inc.) (GCC) ; ", + "glibc_version": "2.11.3", + "hostname": "daint103", + "os_name": "SLES", + "os_type": "Linux", + "os_version": "11_SP3", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.9 (unknown, Apr 7 2015, 08:28:12) ; [GCC 4.3.4 [gcc-4_3-branch revision 152973]]", + "system_gcc_path": "/opt/gcc/4.8.2/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..f6daad29dd --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -0,0 +1,30 @@ +easyblock = "ConfigureMake" + +name = 'magma' +version = '2.0.0' + +homepage = 'http://icl.cs.utk.edu/magma/' +description = "The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems." + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +preinstallopts = "export EBINSTALLPREFIX=%(installdir)s && " + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] + +skipsteps = ['configure'] + +builddependencies = [ ('CMake', '3.5.0'), + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] + +sanity_check_paths={ + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +patches = [('magma-2.0.0.patch')] + +moduleclass = 'math' + diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch new file mode 100644 index 0000000000..1f81da8c77 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch @@ -0,0 +1,106 @@ +diff -ru magma-2.0.0.orig//Makefile magma-2.0.0/Makefile +--- magma-2.0.0.orig//Makefile 2016-02-09 22:06:38.000000000 +0100 ++++ magma-2.0.0/Makefile 2016-03-25 17:35:34.000000000 +0100 +@@ -4,7 +4,7 @@ + # Users should make all changes in make.inc + # It should not be necesary to change anything in here. + +-include make.inc ++include make.inc.openblas + + # defaults if nothing else is given in make.inc + CC ?= gcc +diff -ru magma-2.0.0.orig//make.inc.openblas magma-2.0.0/make.inc.openblas +--- magma-2.0.0.orig//make.inc.openblas 2016-02-09 22:04:46.000000000 +0100 ++++ magma-2.0.0/make.inc.openblas 2016-03-25 17:29:35.000000000 +0100 +@@ -1,72 +1,49 @@ + #////////////////////////////////////////////////////////////////////////////// +-# -- MAGMA (version 2.0.0) -- ++# -- MAGMA (version 1.6.1) -- + # Univ. of Tennessee, Knoxville + # Univ. of California, Berkeley + # Univ. of Colorado, Denver +-# @date February 2016 ++# @date January 2015 + #////////////////////////////////////////////////////////////////////////////// + +-# GPU_TARGET contains one or more of Fermi, Kepler, or Maxwell, ++# GPU_TARGET contains one or more of Tesla, Fermi, or Kepler, + # to specify for which GPUs you want to compile MAGMA: +-# Fermi - NVIDIA compute capability 2.x cards +-# Kepler - NVIDIA compute capability 3.x cards +-# Maxwell - NVIDIA compute capability 5.x cards ++# Tesla - NVIDIA compute capability 1.x cards (no longer supported in CUDA 6.5) ++# Fermi - NVIDIA compute capability 2.x cards ++# Kepler - NVIDIA compute capability 3.x cards + # The default is "Fermi Kepler". +-# Note that NVIDIA no longer supports 1.x cards, as of CUDA 6.5. + # See http://developer.nvidia.com/cuda-gpus + # + #GPU_TARGET ?= Fermi Kepler ++GPU_TARGET = Kepler + +-# -------------------- +-# programs +- +-CC = gcc +-CXX = g++ ++CXX = CC ++CC = cc + NVCC = nvcc +-FORT = gfortran ++FORT = ftn + + ARCH = ar + ARCHFLAGS = cr + RANLIB = ranlib + +- +-# -------------------- +-# flags +- + # Use -fPIC to make shared (.so) and static (.a) library; + # can be commented out if making only static library. + FPIC = -fPIC + +-CFLAGS = -O3 $(FPIC) -DADD_ -Wall -fopenmp +-FFLAGS = -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-F90FLAGS = -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument -x f95-cpp-input +-NVCCFLAGS = -O3 -DADD_ -Xcompiler "$(FPIC)" ++CFLAGS += -DADD_ -DMAGMA_SETAFFINITY ++CXXFLAGS += -DADD_ -DMAGMA_SETAFFINITY ++FFLAGS += -DADD_ -Wall -Wno-unused-dummy-argument ++F90FLAGS += -DADD_ -Wall -Wno-unused-dummy-argument -x f95-cpp-input ++NVCCFLAGS = -O3 -DADD_ -Xcompiler "-fno-strict-aliasing $(FPIC)" + LDFLAGS = $(FPIC) -fopenmp + +-# C++11 (gcc >= 4.7) is not required, but has benefits like atomic operations +-CXXFLAGS := $(CFLAGS) -std=c++11 +-CFLAGS += -std=c99 +- +- +-# -------------------- +-# libraries +- + # gcc with OpenBLAS (includes LAPACK) +-LIB = -lopenblas +- +-LIB += -lcublas -lcusparse -lcudart +- +- +-# -------------------- +-# directories ++LIB = -lcublas -lcusparse + + # define library directories preferably in your environment, or here. +-#OPENBLASDIR ?= /usr/local/openblas +-#CUDADIR ?= /usr/local/cuda +--include make.check-openblas +--include make.check-cuda ++CUDADIR=$(EBROOTCUDA) + + LIBDIR = -L$(CUDADIR)/lib64 \ +- -L$(OPENBLASDIR)/lib + + INC = -I$(CUDADIR)/include ++prefix = $(EBINSTALLPREFIX) -- GitLab From ed68b28d57a933a0570d61aa9a8a7c8d40ebffb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 15:09:50 +0200 Subject: [PATCH 0242/2403] {system}[intel/2016a] file 5.25 + enhance sanity check --- .../easyconfigs/f/file/file-5.17-GCC-4.8.2.eb | 8 +++--- .../f/file/file-5.25-intel-2016a.eb | 25 +++++++++++++++++++ 2 files changed, 29 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb index 63db8305d5..bca5d69508 100644 --- a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb @@ -12,14 +12,14 @@ homepage = 'http://www.darwinsys.com/file/' description = """The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.""" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + source_urls = ['ftp://ftp.astron.com/pub/file/'] sources = [SOURCE_TAR_GZ] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - sanity_check_paths = { - 'files': ['bin/file'], - 'dirs': [] + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] } moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb new file mode 100644 index 0000000000..61f8e29397 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.25' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' -- GitLab From b92eaf3eac50f53ac2b688a53b821a92f797371a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:02:50 +0200 Subject: [PATCH 0243/2403] add easyconfig Java-1.8.0_77.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb new file mode 100644 index 0000000000..fa48d66cd4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_77' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 3df8b5b4e3a15448caa4ef4b023b13d4ee1f31a8 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 16:42:55 +0200 Subject: [PATCH 0244/2403] More style edits suggested by @boegel --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index 94cd13bd81..da99f9d5b8 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -24,17 +24,17 @@ builddependencies = [ ('Autotools', '20150215'), ] dependencies = [ - ('GMP', '6.1.0'), + ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = ('--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' - ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp') +configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' +configopts += ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' sanity_check_paths = { 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 4f0fbad866..22ad6d392a 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -32,7 +32,7 @@ configopts = "--with-gmp=$EBROOTGMP --enable-inline" sanity_check_paths = { 'files': ['bin/givaro-config', 'include/givaro-config.h'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index 640a495db8..f0951b2b35 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ ('FFLAS-FFPACK', '2.2.0'), - ('Givaro', '4.0.1'), + ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " @@ -33,7 +33,7 @@ configopts = "--with-givaro=$EBROOTGIVARO --with-fflas-ffpack=$EBROOTFFLASMINFFP sanity_check_paths = { 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h', 'lib/liblinbox.a'], - 'dirs': ['bin', 'include', 'lib'], + 'dirs': ['bin', 'include', 'lib'], } moduleclass = 'math' -- GitLab From 29197e7d989d93758bf1fb0ee678de15f6d0f592 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2016 16:47:02 +0200 Subject: [PATCH 0245/2403] add easyconfig NGS-1.2.3-intel-2016a.eb --- .../n/NGS/NGS-1.2.3-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb new file mode 100644 index 0000000000..ed0e37836c --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.3' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_77', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' -- GitLab From 96afcdd6c2a927d1aaf5e9364af131a34c1e0162 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Wed, 30 Mar 2016 22:22:41 +0200 Subject: [PATCH 0246/2403] Use `env` wherever `preconfigopts is used to set environmental variables. Without `env`, we are relying on a syntactical feature of Bourne-type shells; the `env` utility guarantees that the command-line will continue to work even with other shells (e.g., `tcsh`). --- .../easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- .../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb | 2 +- .../Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb | 2 +- .../g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 2 +- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb | 2 +- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 2 +- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- 105 files changed, 105 insertions(+), 105 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb index 20c30c8e62..6b5c1c6d52 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -31,7 +31,7 @@ dependencies = [ ('Boost', '1.58.0', versionsuffix), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTSPARSEHASH/include' sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index 13ae69456f..916fcd7e48 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 5144a9afc9..97e5c8330b 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 3b963e0d7e..74f9dffca6 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -25,7 +25,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index f6a35a3dc0..efd5845e70 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('gperf', '3.0.4'), ] -preconfigopts = 'EMACS=no' +preconfigopts = 'env EMACS=no' configopts = '--with-gnu-gettext' sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 608c44a155..35e328daad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 17ecd5c190..6c55f76694 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 61254037e0..6f9a318360 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 0007322f1f..ef80ad6bb5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -20,7 +20,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e6f5a84c78..b8fa0b77ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 8efdae380a..9ec199023d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -22,7 +22,7 @@ builddependencies = [ ] # statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index b6d188a41b..63837a712c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 40e3ccc1a8..cfcfe38d3d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib # further, add the system library path in the rpath: this should 'harden' the # resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' prebuildopts = preconfigopts # make sure that system libraries are also considered by ld and ld.gold is also built diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 501824903b..7b8dca8554 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -34,7 +34,7 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index d258537699..2ef873d2da 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 645f94a833..25b9208f0e 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -32,7 +32,7 @@ dependencies = [ patches = ['Cufflinks_GCC-4.7.patch'] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb index 799e9172ba..9c37cd717b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' configopts += ' --enable-intel64 ' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb index 991b5a4c8b..6751cec530 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index d0372e6f70..6ac33d77d4 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 2741497a4d..e368245a6c 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb index 0a4b6fa7ab..fe15c228e1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +preconfigopts = 'env CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb index 43da714323..50fce481a6 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +preconfigopts = 'env CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb index 38e9d1ce03..8360322002 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2015b-Python-2.7.10-Boost-1.59.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] configopts = '--enable-intel64 --with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' -preconfigopts = 'CPPFLAGS=-I${EBROOTEIGEN}/include' +preconfigopts = 'env CPPFLAGS=-I${EBROOTEIGEN}/include' sanity_check_paths = { 'files': ['bin/cufflinks'], diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb index ffd2e3a7a6..4bcdb9773b 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb index 8f6396f5b8..7a4d21e078 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb index ee472aa372..4e298ad677 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb index ef2423ee53..4b6a000d12 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb index c0f9f1c6d8..9445690c85 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb index 384aa93ebf..1f66eb79d7 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb @@ -17,7 +17,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb index 048ac9570d..8bc580fd82 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('JasPer', '1.900.1'), ] -preconfigopts = 'FC=$F90' +preconfigopts = 'env FC=$F90' configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb index cc9e86a7d0..8c554c3e24 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20140805-GCC-4.9.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://www.prevanders.net'] dependencies = [('libelf', '0.8.13')] with_configure = True -preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' configopts = "--enable-shared " # This is dirty but libdwarf cannot find it's own library in the build process... diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 6ac9b7d5c3..01c9c7b5d7 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb index a021127537..3c63b87470 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 11090d4b7a..437954d342 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb index f66aff6454..f0291301fc 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb index f03e2b9b60..e43c36e89c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 33c34a406a..834a292992 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index 7e3d115240..c3e51b6854 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index ce77f3502c..8f259d339a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index e28f16cff6..5f22d77a36 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index 2a5e9c8d05..ea05edcced 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 4281029487..1af83efe66 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index 2ac72299c5..c0a23d9702 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 17ca0fce10..084f645370 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 8d2ea29b4c..f0751a5aa2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index aea7099ee4..0ae01c0783 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 7216c9ca1c..39cc896311 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb index 6589e3ba7c..9a9c4dd1a0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index a36ac06d74..245f1b2b64 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 4425696364..8e8d97c9af 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 8892dfc907..0e2ab07ab0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 7778abffff..c6a66c33d9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 157a15b6bb..f765c40888 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 6a9bcf9cdd..f13cdef958 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index c5324cbad1..f5f1c5bd47 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb index b07b7634b9..5c9d193cce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 853816b19b..596222a189 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 26cadb84b9..2ed024170c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 055d457da0..fd8d7fabf0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 6f9a153abf..35b967c78d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index a4bce470a5..54fd902c42 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 8003f03676..12e011a8ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 15a227218e..18ebd1a1e7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb index 9236fd84d0..cdb4bf6f5a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7435fb5029..0f7e912805 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index a669b4f5be..27560c2cd2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index a120dd4307..7ca975dc76 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 883868add2..b30099a775 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index d828f262a5..712eabaeda 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 252a86c527..667201ed1a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -17,7 +17,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb index afd0f9f313..55974b6b67 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb index 46e89b5a96..68d5cccacb 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.25')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb index 05d8476935..d726fb4329 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb index 362df4f9bd..2745ab8557 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 763ccd9488..c856b61000 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb index d3b76459b6..b5740c5333 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb index 66ecad79ff..4bbd90baa7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb index 037141ab77..e33a1ae239 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb index fb2145ca85..675e8c38cd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 8845b7c009..dbc0087596 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb index 793dcaf0af..cbb20595ce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb index e594babc96..7ecfe2dc0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.14.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb index ec5413615c..3c009a2b02 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb index 35af50be83..84703a1b03 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.2.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb index 2db2e85326..fdf5247663 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb @@ -20,7 +20,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb index c9c675d484..fb685e3854 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.1.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb index 46eef59b19..68d21572c3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb index 583b41298f..76b828f76d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb index 3e67c20449..9539bb724f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb index 2c8752c400..051672a6f2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb index de76493eec..fa9c58b0b8 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb index 0762f90f29..5b1cb39b0a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016a.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 5bcb7de6da..b08de1e59f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -15,6 +15,6 @@ checksums = ['5dc58ed08fd3142c260b70fe297e127c'] builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs -preconfigopts = 'LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' +preconfigopts = 'env LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb index 9cac08c076..3b2363cdf9 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.4-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb index c6b4f4fabd..b547dd35fb 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.0-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb index f3480b9f42..2be6013ea4 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb index a8664f7399..c2a88ca7fa 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('libmatheval', '1.1.11'), ] -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = ' --exec-prefix=%(installdir)s --enable-gsl' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index bcf88e98c9..a7caba4fae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] configopts = ' --enable-unicode=ucs4 ' -preconfigopts = ' LDFLAGS="-lstdc++" ' +preconfigopts = 'env LDFLAGS="-lstdc++" ' # libffi build in python is still broken, see http://bugs.python.org/issue4130 patches = ['python-2.7_libffi-include-xmmintrin.patch'] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 4f0b4fda48..05baffbd16 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -34,7 +34,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 59556c19fd..fc6f18713c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -32,7 +32,7 @@ dependencies = [ ] # use external ZLIB -preconfigopts = 'ZLIB=$EBROOTZLIB ' +preconfigopts = 'env ZLIB=$EBROOTZLIB ' # architecture arch = 'linuxx8664icc' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 740784c812..795671412f 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 327bd773eb..1e20cf23ec 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index 375b58016f..b7723d7af3 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index 316c43df98..a66be3332b 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -32,7 +32,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index d9a8ebec92..664ec56172 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA-2.1.6_ictce.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' +#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', -- GitLab From 53eadadc575930bd0d5729d2239c3df8d70316fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 10:16:47 +0200 Subject: [PATCH 0247/2403] add easyconfig ncbi-vdb-2.5.8-1-intel-2016a.eb --- .../ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb new file mode 100644 index 0000000000..4197805f9e --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-intel-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.5.8-1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.3'), + ('file', '5.25'), # provides libmagic + ('HDF5', '1.8.16'), + ('NGS', '1.2.3'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0af7e722e8f3aa0b28b12b62424772425ad587bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 11:57:16 +0200 Subject: [PATCH 0248/2403] add easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- .../h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb new file mode 100644 index 0000000000..c08c2f92a9 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.3-beta' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['deb29e32e48045b2f970fb999946b411'] + +dependencies = [ + ('NGS', '1.2.3'), + ('ncbi-vdb', '2.5.8-1'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e0707b966ea23e736726488c4039e47960fc9bbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:22:31 +0200 Subject: [PATCH 0249/2403] modify easyconfig HISAT2-2.0.3-beta-intel-2016a.eb --- easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb index c08c2f92a9..ab9ee05adb 100644 --- a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.3-beta-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncbi-vdb', '2.5.8-1'), ] -buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB" +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] -- GitLab From 3120311ff75bf2561aa7b6cfee5f6f3456966d47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 12:47:43 +0200 Subject: [PATCH 0250/2403] {bio}[intel/2016a] NGS-Python 1.2.3 --- ...-Python-1.2.3-intel-2016a-Python-2.7.11.eb | 46 +++++++++++++++++++ .../NGS-Python-1.2.3_fix-prefix.patch | 13 ++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..94dc61a1a7 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'NGS-Python' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['NGS-Python-%(version)s_fix-prefix.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('NGS', version), + ('ncbi-vdb', '2.5.8-1'), +] + +preconfigopts = "cd ngs-python && " + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS " +configopts += "--with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-python' +installopts = "-C ngs-python" + +parallel = 1 + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python2.7/site-packages', 'share/examples-python'], +} + +sanity_check_commands = [('python', "-c 'import ngs'")] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch new file mode 100644 index 0000000000..60411ef541 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-1.2.3_fix-prefix.patch @@ -0,0 +1,13 @@ +correctly specify prefix to install NGS-Python package to +author: Kenneth Hoste (HPC-UGent) +--- ngs-1.2.3/ngs-python/Makefile.python.orig 2016-03-31 12:34:54.124551782 +0200 ++++ ngs-1.2.3/ngs-python/Makefile.python 2016-03-31 12:37:01.515699327 +0200 +@@ -82,7 +82,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) -- GitLab From af36210e03039665d0ac97e321a93585e12c0f2a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:11:56 +0100 Subject: [PATCH 0251/2403] Add explicit Python dep and rename to reflect that --- ...6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb} (98%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb similarity index 98% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index c33eb72992..4fc2b27c34 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -26,6 +26,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('R', '3.2.3'), + (python, pyver), ('numpy', '1.10.1', versionsuffix), ] -- GitLab From 311923d8aa7e6717ee43fa4414580f5e4cf9f605 Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:11:59 +0200 Subject: [PATCH 0252/2403] Use `env` wherever `preinstallopts is used to set environmental variables. --- .../p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb index 699eafed53..ab6efabad7 100644 --- a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.29-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ skipsteps = ['configure', 'build'] # redefine $HOME to specify installation prefix O_o -preinstallopts = "HOME=%(installdir)s make local &&" +preinstallopts = "env HOME=%(installdir)s make local &&" sanity_check_paths = { 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], -- GitLab From 2fb5725bfc6410ec511fdfa3183ba32d6161dd14 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 12:47:26 +0100 Subject: [PATCH 0253/2403] Fix Subread filename to match version --- ...bread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} | 0 ...bread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2015b.eb => Subread-1.5.0-p1-foss-2015b.eb} (100%) rename easybuild/easyconfigs/s/Subread/{Subread-1.5.0p1-foss-2016a.eb => Subread-1.5.0-p1-foss-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2015b.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/s/Subread/Subread-1.5.0p1-foss-2016a.eb rename to easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb -- GitLab From 476581ab23b45a00bb8d8a5bd7e94fad980ed7be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:42:24 +0200 Subject: [PATCH 0254/2403] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 2.7.11 --- ...reenlet-0.4.9-intel-2016a-Python-2.7.11.eb | 30 ++++++++++++++++ .../libsodium/libsodium-1.0.6-intel-2016a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 28 +++++++++++++++ ...Q-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb | 28 +++++++++++++++ ...SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 27 ++++++++++++++ .../util-linux-2.27.1-intel-2016a.eb | 33 +++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb | 35 +++++++++++++++++++ 7 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c8fb9489f2 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb new file mode 100644 index 0000000000..8cd02bafe0 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.6' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb new file mode 100644 index 0000000000..7d687c23fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..3b84d83e0c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..159567d24d --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb new file mode 100644 index 0000000000..fa18d8bb1d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb new file mode 100644 index 0000000000..5eeb602737 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.6'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 227f6059951a467bb27eecc6f54afda8284eef69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 14:48:42 +0200 Subject: [PATCH 0255/2403] {tools}[intel/2016a] SCOOP 0.7.1.1 w/ Python 3.5.1 --- ...Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 30 +++++++++++++++++++ ...MQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb | 28 +++++++++++++++++ .../SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 27 +++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..26ba01fae4 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb new file mode 100644 index 0000000000..40389161f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-intel-2016a-Python-3.5.1-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..8eac309517 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('Greenlet', '0.4.9', versionsuffix), + ('PyZMQ', '15.2.0', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 31497fc893cc738df14f49f87e60e92868d78313 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:31 +0200 Subject: [PATCH 0256/2403] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb index 8eac309517..21ced6bf47 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-3.5.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 43ac5b3c6c64f1f65f61be34acdb65097e0a2ba1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:27:48 +0200 Subject: [PATCH 0257/2403] fix sanity check for SCOOP --- .../s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb index 159567d24d..eb5338d376 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-intel-2016a-Python-2.7.11.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s.release-py%(pyshortver)s.egg'], + 'files': ['lib/python%(pyshortver)s/site-packages/scoop-%(version)s-py%(pyshortver)s.egg'], 'dirs': [], } -- GitLab From 7f64fcc96a1ceb19d3f513d26b534cf3e9b36897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:29:01 +0200 Subject: [PATCH 0258/2403] fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 26ba01fae4..0d6aba002e 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,7 +22,7 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', 'lib/python%(pyshortver)s/site-packages/greenlet.so'], 'dirs': [], } -- GitLab From eb191c8e53282e75113408cb024eb7063c4df418 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 15:32:28 +0200 Subject: [PATCH 0259/2403] really fix sanity check for Greenlet --- .../g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb index 0d6aba002e..26eafeafb1 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.9-intel-2016a-Python-3.5.1.eb @@ -22,9 +22,8 @@ patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] dependencies = [('Python', '3.5.1')] sanity_check_paths = { - 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h', - 'lib/python%(pyshortver)s/site-packages/greenlet.so'], - 'dirs': [], + 'files': ['include/python%(pyshortver)sm/greenlet/greenlet.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'devel' -- GitLab From a671d34e8d9ffcacff21ea8076804301a2e037cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 16:24:05 +0200 Subject: [PATCH 0260/2403] don't hardcode .so in OpenPGM easyconfig --- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb index 7d687c23fb..d391dfe9fd 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -21,7 +21,7 @@ configopts = '--with-pic' start_dir = 'pgm' sanity_check_paths = { - 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], 'dirs': ['include'], } -- GitLab From 9771b3cbc1b41f77c6bc468f521a821c3b7c2b1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:00:48 +0200 Subject: [PATCH 0261/2403] add zlib as explicit dep in Tk easyconfigs --- easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb | 1 + .../easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 + 29 files changed, 50 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb index 9ebfd37f5f..ff05f0890c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-foss-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb index 5f035ccbf2..e28fd7a2dc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb index 16d5293528..cbf7bcb4b2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb index 1415c70f4e..06a1978ba4 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb index 5c0a6ccd92..4798d6cf81 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb index f65e1a0e09..71f6f47992 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb index 25372ffd8f..11e23b0c07 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-intel-2014b.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb index 3231de70b9..8b45a8770e 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.5'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb index a79397a5f8..60130e9216 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -dependencies = [('Tcl', version)] +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.7'), +] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 602101704a..878cfecf53 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 8ff29d34a2..ac0d5ff0bc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb index c34f24fd99..0cf00324c8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb index 31e024fb43..aaa247a658 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index a292e06eb8..0a860475e3 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index cd4da6afb6..890bfc8cfe 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb index 025f5e6476..6550c8a427 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb index d841e7bd84..4762abfa09 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb index a8245c8580..684f3bddb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb index 05eafdb2e8..f077e32cc2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb index da82b39576..9e3efc89f0 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb index c10f179e0c..89ecb3248a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb index 7aa028f61c..5066a5847c 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb index b3fd0e9714..9419fc66d6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb index 7feeb34477..60f899a584 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb index 4630a6a0f4..53f70e54d2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 6e8ab4a8ff..85504f8688 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb index 6b8350fb20..b7e6c77202 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb index 8ada7cd405..c0f2464a6d 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-libX11-1.6.3.eb @@ -24,6 +24,7 @@ builddependencies = [ dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), (libx11, libxver), ('libXt', '1.1.5'), ('libXext', '1.3.3'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9f46cbbff7..9eede49210 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -17,6 +17,7 @@ patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), + ('zlib', '1.2.8'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From ac6e72b23b9ffd5642a04710023df6f515bcfd9a Mon Sep 17 00:00:00 2001 From: Riccardo Murri Date: Thu, 31 Mar 2016 13:05:24 +0200 Subject: [PATCH 0262/2403] Use `env` wherever `prebuildopts is used to set environmental variables. --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb | 2 +- 24 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 35e328daad..c3ffc6e24a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 6c55f76694..418f81f5f1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 6f9a318360..2e680c9ce3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index ef80ad6bb5..b6d6a68fc6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -21,7 +21,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index b8fa0b77ca..6858b124b1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -22,7 +22,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 9ec199023d..5378940837 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -23,7 +23,7 @@ builddependencies = [ # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 24f4ba27ec..7278d23d80 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,7 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'FFLAGS="$FFLAGS -fpp"' +prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' modextrapaths = {'PATH': 'FDS_Compilation'} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 2c72b2e6f5..17513817cb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1a69d47441..1e7fe202e8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 9d960059a5..43f9b4f3d2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 73b355c719..7fe4602968 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 72d772f450..3ddc492ea7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3ee16e73ea..3fe5e0bc06 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 0cd27019ac..442c4168fe 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index a724cb0c52..82b8af7b4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 70a2816d6b..7c42ab711a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index 0371483898..ed80bbbf2f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 7e87cc2bd4..663c38a45e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 9c7388d824..3df094cda8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb index 3f8c039cdb..0df4d93ef0 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb index e493e1ad48..5bb00f47ad 100644 --- a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] dependencies = [('zlib', '1.2.8')] -prebuildopts = 'CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' +prebuildopts = 'env CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' files_to_copy = [(['bin/Minimac3'], 'bin')] diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb index 6d97e3c57a..ea8c9d49ac 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-goolf-1.4.10.eb @@ -38,7 +38,7 @@ builddependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb index 36d9829a6d..4476f0d922 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb @@ -38,7 +38,7 @@ dependencies = [ ] # make has problems with utf8 -prebuildopts = "LANG=C " +prebuildopts = "env LANG=C " # motif ships a broken automake and libtool preconfigopts = "rm -f libtool install-sh missing depcomp config.guess config.sub && " diff --git a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb index e8dddb718d..eb272b1b70 100644 --- a/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/m/multitail/multitail-6.2.1-intel-2015a.eb @@ -21,7 +21,7 @@ files_to_copy = [ dependencies = [("ncurses", "5.9")] -prebuildopts = 'DESTDIR=%(installdir)s ' +prebuildopts = 'env DESTDIR=%(installdir)s ' sanity_check_paths = { 'files': ['bin/multitail'], -- GitLab From 27192c656261f1cfaea193869f34d7afdd7a4d81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:28:35 +0200 Subject: [PATCH 0263/2403] don't hard overwrite $CPATH in prebuildopts in Mesa easyconfig files --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 2 +- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 17513817cb..3f895315b2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -59,7 +59,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place #preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 1e7fe202e8..592c4a1182 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -57,7 +57,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 43f9b4f3d2..2bd0ff0f94 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 7fe4602968..a22cf02d69 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -56,7 +56,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disabl #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 3ddc492ea7..171b47710c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3fe5e0bc06..3282ad740c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 442c4168fe..c47447d239 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 82b8af7b4f..57483e1d4f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -43,7 +43,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index 7c42ab711a..fa63661948 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb index ed80bbbf2f..3d2d9d7e93 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.1.13-Python-2.7.3.eb @@ -44,7 +44,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 663c38a45e..ac83c1243a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 3df094cda8..810e10d3bb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -45,7 +45,7 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demo # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', -- GitLab From 15c44bd734ed1e058bd228a60cd39beab076ee84 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 17:36:49 +0100 Subject: [PATCH 0264/2403] Style fixes for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 3 +-- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4fd69f051e..4df6c05b5e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +startdir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index 1312eb0648..f0d2074639 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -prebuildopts = 'cd src;' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] - sanity_check_paths = { 'files': ['LICENSE', 'README.txt'], 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] -- GitLab From 7fc04b6a034430ccc672bcc4fd954b7efd947704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 18:53:50 +0200 Subject: [PATCH 0265/2403] use existing libxml2 easyblock, use %(pyver)s --- .../l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb index 0237c8f83b..0df5cbd957 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,6 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -18,13 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' -- GitLab From 0d6511bd1d3ba7dcafa852dc033de9aff737a052 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:05:34 +0100 Subject: [PATCH 0266/2403] Use new-style pyver and make sanity_check paths more specific --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb index 4fc2b27c34..a177369637 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb @@ -6,6 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -20,21 +21,17 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -python = 'Python' -pyver = '2.7.10' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ ('R', '3.2.3'), - (python, pyver), - ('numpy', '1.10.1', versionsuffix), + ('Python', '2.7.10'), ] runtest = "python setup.py test" sanity_check_paths = { - 'files': [], - 'dirs': ["bin", "lib"] + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', + 'bin/split_paired_bam.py'], + 'dirs': ['lib'] } options = {'modulename': 'qcmodule'} -- GitLab From e991040ec94fd7b22bab054ff840999434975cd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2016 19:06:51 +0200 Subject: [PATCH 0267/2403] consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs --- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 31c851b3d9..8398e40d06 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index 3010711346..b84761b602 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b62284872a..b4bb4c955d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index c2e9e52426..5df1dda5a3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index 90c7eb9017..f406268a87 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index a79d153988..560606e07a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 372d1c346d..00b1eb05a8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index 0fa72c61c9..a939e01023 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 89984f9baf..64c98aad33 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 52fc84e052..745063ebad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index e856a3fd43..a95ac9f601 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index e2764250bf..134d181212 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index ad83091b2b..25f9aacace 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index e83b261924..5ca90d16a7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 94ec58056b..4abe05a74f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index 411820a76b..f58173164e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index b66775c7a6..6a7048dcf1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index 42808d7b77..aa806c1087 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 3b4187acd1..304b160de5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index e8d95f1f54..46c1b375cb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 68b3d851f6..0289e6c40e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index d6a8a6e705..857e1b9ffc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index f842bdc90a..a805266216 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 292da57c7e..6746b4b3a4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 519be6b6b3..4472772492 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index 37a6837b2b..104ad6a3bd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 3f396ce26b..2bc8d9c022 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2469d572c2a76c37fc5fb46c174678e48b6c85c8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 18:32:03 +0100 Subject: [PATCH 0268/2403] Add R suffix and fix sanity_check style --- ....10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/RSeQC/{RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb => RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb} (89%) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb similarity index 89% rename from easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index a177369637..58d91e5c53 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -7,6 +7,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' versionsuffix = '-Python-%(pyver)s' +versionsuffix += '-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can @@ -29,8 +30,7 @@ dependencies = [ runtest = "python setup.py test" sanity_check_paths = { - 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', - 'bin/split_paired_bam.py'], + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], 'dirs': ['lib'] } -- GitLab From 6027c4ad03cf95b635270fa365e376735c183426 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 13:47:56 -0500 Subject: [PATCH 0269/2403] Renamed Easyconfig file from gtool-0.7.5-linux_x86_64.eb to gtool-0.7.5_linux_x86_64.eb --- .../{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/gtool/{gtool-0.7.5-linux_x86_64.eb => gtool-0.7.5_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5-linux_x86_64.eb rename to easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb -- GitLab From 61839ae12b5c739ec3e36b4ee971cd5e4da2d3f8 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Thu, 31 Mar 2016 14:18:10 -0500 Subject: [PATCH 0270/2403] Renamed Easyconfig file from shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb to shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb --- ...-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb => shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-v2.r837_GLIBCv2.12-linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb -- GitLab From 4df62bb5e637f584d3ebffb56b2fd25d40a94b2b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:11:56 +0100 Subject: [PATCH 0271/2403] Use start_dir, not startdir for Subread --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 4df6c05b5e..5192855877 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -startdir = 'src &&' +start_dir = 'src &&' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 6dfc122e053950dd94d862cb80be20a6797e4e12 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Mar 2016 22:35:29 +0100 Subject: [PATCH 0272/2403] Style cleanup for versionsuffix --- .../r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index 58d91e5c53..d3a31d723c 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -6,8 +6,7 @@ easyblock = 'PythonPackage' name = 'RSeQC' version = '2.6.3' -versionsuffix = '-Python-%(pyver)s' -versionsuffix += '-R-%(rver)s' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' homepage = 'http://rseqc.sourceforge.net/' description = """RSeQC provides a number of useful modules that can -- GitLab From 37491f387e1a294625a7d71fa72bd06065326dba Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 1 Apr 2016 10:10:53 +0100 Subject: [PATCH 0273/2403] Fix start_dir --- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 5192855877..612c514399 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index f0d2074639..e525a015c8 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] -start_dir = 'src &&' +start_dir = 'src' buildopts = '-f Makefile.Linux' files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] -- GitLab From 2e4f5401e6f65f307bbfced75186d8a0f43aba91 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:00:50 -0500 Subject: [PATCH 0274/2403] Converting from 'Binaries' Easyblock to 'Tarball'. --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index 6d1dad133e..bc3ceffb75 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'gtool' version = '0.7.5' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xvf gtool_v%(version)s_x86_64.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 163189467710769bcb3fc8785cfc0bc719ab8ac1 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 1 Apr 2016 11:07:32 -0500 Subject: [PATCH 0275/2403] Converting from 'Binaries' Easyblock to 'Tarball'. --- .../s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 7441bd58af..75a894a8c8 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "Tarball" name = 'shapeit' version = '2.r837.GLIBCv2.12' @@ -16,10 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] sources = ['shapeit.v%(version)s.Linux.static.tgz'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "tar xzvf shapeit.v%(version)s.Linux.static.tgz && HOME=%(builddir)s && " -install_cmd += "cp -a %(builddir)s/* %(installdir)s" - sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], 'dirs': ["example"] -- GitLab From 53eccaea377809af2cf69d87b18ef86843a6cf79 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:05:44 -0700 Subject: [PATCH 0276/2403] add easyconfig for LAME MP3 encoder --- .../l/LAME/LAME-3.99.5-foss-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb new file mode 100644 index 0000000000..8ce773805a --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '5.9')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From d07bf5d6c4a52bb9f65d5d8add7c300ce05b084d Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 09:21:03 +0200 Subject: [PATCH 0277/2403] qt/486 for dummy toolchain --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb new file mode 100644 index 0000000000..5c83d337b8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -0,0 +1,15 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] +sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] + +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +platform = 'linux-g++-64' + +moduleclass = 'devel' -- GitLab From 686957e8a63d021e32cc88fe2a96e09e131651e2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 00:42:51 -0700 Subject: [PATCH 0278/2403] Pygments: fix homepage URL and description --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 4 ++-- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index 103bb38998..dc2b7c311c 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 06251d7872..45a6907cbe 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -3,8 +3,8 @@ easyblock = 'PythonPackage' name = 'Pygments' version = '2.0.2' -homepage = 'https://pypi.python.org/pypi/requests/2.6.0' -description = """Python http for humans""" +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 9e88f53c5f8c8aa7540c08f84b5c96a77d720fd1 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:14:43 +0200 Subject: [PATCH 0279/2403] fixing line max length --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 5c83d337b8..48c0604f80 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 79a0eb02eaac79c6058e84ca25a9326a731c1970 Mon Sep 17 00:00:00 2001 From: jgp Date: Sat, 2 Apr 2016 14:29:52 +0200 Subject: [PATCH 0280/2403] adding -no-webkit for redhat builds --- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 48c0604f80..eacf9a8384 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -9,8 +9,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' -configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' platform = 'linux-g++-64' moduleclass = 'devel' -- GitLab From 05a5e0a091c4191a14cac7cf03367874b7e20eae Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 20:53:00 -0700 Subject: [PATCH 0281/2403] add easyconfig for FLAC audio codec --- .../f/FLAC/FLAC-1.3.1-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb new file mode 100644 index 0000000000..72f2e62fcc --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.1' + +homepage = 'https://xiph.org/flac/' +description = """Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://downloads.xiph.org/releases/flac/'] + +sanity_check_paths = { + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 28b3cea3b180c4b84704914f72a04857aaa980f5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sat, 2 Apr 2016 21:08:27 -0700 Subject: [PATCH 0282/2403] add easyconfig for SoX (a Torch7 dependency) --- .../s/SoX/SoX-14.4.2-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb new file mode 100644 index 0000000000..8228308a17 --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://http://sox.sourceforge.net/' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] + +# These are not strictly mandatory but add flac and mp3 support to SoX +dependencies = [ + ('FLAC', '1.3.1'), + ('LAME', '3.99.5') +] + +sanity_check_paths = { + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From f42683f08dedc4e4c9980e0d116ef92403cbc805 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Apr 2016 14:01:34 +0200 Subject: [PATCH 0283/2403] add easyconfig scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb --- ...-learn-0.17.1-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..50d044b41c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 65c8245f61d91344b4965fe2f35a153fee92de78 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:51:25 -0700 Subject: [PATCH 0284/2403] FLAC: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 72f2e62fcc..509bb248c0 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] sanity_check_paths = { - 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.so'], + 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From dddf87803d9b9f070568fdefa07f7a2325437c23 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 09:54:55 -0700 Subject: [PATCH 0285/2403] Pygments: keep lines under 120 characters --- .../p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 3 ++- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb index dc2b7c311c..bfe92c90eb 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index 45a6907cbe..3c3f9ad92d 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,8 @@ name = 'Pygments' version = '2.0.2' homepage = 'http://pygments.org/' -description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.""" +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From c4186634b8ced2d454d53bad348efcde85150ff3 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:11:01 -0700 Subject: [PATCH 0286/2403] use SHLIB_EXT rather than .so --- easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb index 8ce773805a..a1da0d2c90 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -23,7 +23,7 @@ dependencies = [('ncurses', '5.9')] configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " sanity_check_paths = { - 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.so'], + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 4505dcb1a2b2ccb0274b3e7dc991244ca376ec8e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Sun, 3 Apr 2016 10:20:21 -0700 Subject: [PATCH 0287/2403] SoX: use SHLIB_EXT rather than hardcoding .so --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb index 8228308a17..a71ba0bca6 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -24,7 +24,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.so'], + 'files': ['bin/sox', 'include/sox.h', 'lib/libsox.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From a9481ca6559314b4ddf261a8030df7426a7e3251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Apr 2016 10:57:07 +0200 Subject: [PATCH 0288/2403] add binutils as build dep for FLAC, also run tests --- easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 509bb248c0..76be36ffc6 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -17,6 +17,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://downloads.xiph.org/releases/flac/'] +# use of assembly routines requires a recent binutils +builddependencies = [('binutils', '2.25', '', ('GCC', '4.9.2'))] + +runtest = 'check' + sanity_check_paths = { 'files': ['bin/flac', 'include/FLAC/all.h', 'lib/libFLAC.%s' % SHLIB_EXT], 'dirs': [], -- GitLab From e20aeaca67693bf5be63cd89953e98b9071642dd Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:03:55 -0500 Subject: [PATCH 0289/2403] Changed software name to uppercase (to match the official software name) --- easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb index bc3ceffb75..8b1697e3af 100644 --- a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb +++ b/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb @@ -4,12 +4,12 @@ easyblock = "Tarball" -name = 'gtool' +name = 'GTOOL' version = '0.7.5' -versionsuffix = '_linux_x86_64' homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' -description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ +description = """ GTOOL is a program for transforming sets of genotype data for use with +the programs SNPTEST and IMPUTE. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From b9707b6147bbd5662971c333ff5a371bf7624483 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:13:29 -0500 Subject: [PATCH 0290/2403] Changed the name to SHAPEIT(uppercase), to match the official software name as well as added GLIBCv2.12 part as a versionsuffix --- .../shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb index 75a894a8c8..f2424bbea4 100644 --- a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb +++ b/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb @@ -4,17 +4,18 @@ easyblock = "Tarball" -name = 'shapeit' -version = '2.r837.GLIBCv2.12' -versionsuffix = '_linux_x86_64' +name = 'SHAPEIT' +version = '2.r837' +versionsuffix = '.GLIBCv2.12' homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' -description = """ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. """ +description = """SHAPEIT is a fast and accurate method for estimation of +haplotypes (aka phasing) from genotype or sequencing data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] -sources = ['shapeit.v%(version)s.Linux.static.tgz'] +sources = ['shapeit.v%(version)s%(versionsuffix)s.Linux.static.tgz'] sanity_check_paths = { 'files': ["bin/shapeit", "LICENCE"], -- GitLab From acd19f1aef37e3efbdc6afb2aa3393f73d6a6e5e Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 10:57:50 -0500 Subject: [PATCH 0291/2403] Renamed the Easyconfig file --- .../g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool/gtool-0.7.5_linux_x86_64.eb => GTOOL-0.7.5.eb} (100%) diff --git a/easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb b/easybuild/easyconfigs/g/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/gtool-0.7.5_linux_x86_64.eb rename to easybuild/easyconfigs/g/GTOOL-0.7.5.eb -- GitLab From e11bdeb3d103cd2b7bfd0538ba674537d47fd89c Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:06:12 -0500 Subject: [PATCH 0292/2403] Renamed the Easyconfig file --- easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{ => gtool}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb -- GitLab From 4f08e6223419bd817ec1345de6bf367d0bdccac7 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:10:38 -0500 Subject: [PATCH 0293/2403] Renamed the Easyconfig file --- ...37.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/shapeit/{shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb => SHAPEIT-2.r837.GLIBCv2.12.eb} (100%) diff --git a/easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb b/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/shapeit-2.r837.GLIBCv2.12_linux_x86_64.eb rename to easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From d21d922f81159e6d35ae23969d32b56797458ac4 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:40:26 -0500 Subject: [PATCH 0294/2403] Renamed the directory from 'gtool' to 'GTOOL' --- easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{gtool => GTOOL}/GTOOL-0.7.5.eb (100%) diff --git a/easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gtool/GTOOL-0.7.5.eb rename to easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb -- GitLab From 03d799432b512447956e6f35f56370817d04b817 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 11:42:44 -0500 Subject: [PATCH 0295/2403] Renamed the directory from 'shapeit' to 'SHAPEIT' --- .../s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{shapeit => SHAPEIT}/SHAPEIT-2.r837.GLIBCv2.12.eb (100%) diff --git a/easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb similarity index 100% rename from easybuild/easyconfigs/s/shapeit/SHAPEIT-2.r837.GLIBCv2.12.eb rename to easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb -- GitLab From 64c78cbac01a04a0771040e2cf3ccfa69aa16c14 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Mon, 4 Apr 2016 12:44:17 -0500 Subject: [PATCH 0296/2403] Adding 'modextrapaths' parameter to include the root directory in the PATH variable --- easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb index 8b1697e3af..69e22e6cab 100644 --- a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] +modextrapaths = {'PATH': ''} + sanity_check_paths = { 'files': ["gtool", "LICENCE"], 'dirs': ["example"] -- GitLab From 6057e0642b6b7e61c5e68a69c1709d485e17a6c9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:44:50 -0400 Subject: [PATCH 0297/2403] libxcb-1.11.1 easyconfig for foss-2016a --- .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..b12be025db --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('pkg-config', '0.29'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 3c13fbcd743487e7e4fd7ecc7faa633e07d827d2 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:53:45 -0400 Subject: [PATCH 0298/2403] xproto-7.0.28 easyconfig for foss-2016a --- .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 76dbf608ede3b5ec4fc28fb94e93b9ce633e50ad Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:56:17 -0400 Subject: [PATCH 0299/2403] libpthread-stubs-0.3 easyconfig for foss-2016a --- .../libpthread-stubs-0.3-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From d9ec15efee75c4133c9b4476d5eca278ee28bfb5 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 15:59:14 -0400 Subject: [PATCH 0300/2403] libXau-1.0.8 easyconfig for foss-2016a --- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..b6f23c9a07 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 0ee9e5f553a8df087774e50b56875a009b0c96b9 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:00:39 -0400 Subject: [PATCH 0301/2403] libXdmcp-1.1.2 easyconfig for foss-2016a --- .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..9e90ec9775 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('pkg-config', '0.29') +] + +dependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 76339fa83cdd28958c5dd3e44282321dffaa260c Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Tue, 5 Apr 2016 16:01:47 -0400 Subject: [PATCH 0302/2403] pkg-config-0.29 easyconfig for foss-2016a --- .../pkg-config/pkg-config-0.29-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb new file mode 100644 index 0000000000..2796515752 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 508d9ac2b09b1bffc86709993300f41fee471478 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 5 Apr 2016 15:23:39 -0500 Subject: [PATCH 0303/2403] Changing the file name and the folder name containing it. --- .../MRIcron-06_22_15.eb} | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/m/{mricron/mricron-062215-linux_x86_64.eb => MRIcron/MRIcron-06_22_15.eb} (60%) diff --git a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb similarity index 60% rename from easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a7fb738545..097d50c5b6 100644 --- a/easybuild/easyconfigs/m/mricron/mricron-062215-linux_x86_64.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -4,20 +4,22 @@ easyblock = "Binary" -name = 'mricron' -version = '062215' -versionsuffix = '_linux_x86_64' +name = 'MRIcron' +version = '06_22_15' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' -description = """ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ +description = """ MRIcron allows viewing of medical images. It +includes tools to complement SPM and FSL. Native format is NIFTI +but includes a conversion program (see dcm2nii) for converting DICOM images. +Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] -# Following commands are used to untar the file and copy the content to install directory -install_cmd = "unzip lx.zip && HOME=%(builddir)s && " +# Following commands are used to unzip the files and copy the content to install directory +install_cmd = "unzip lx.zip &&" install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { -- GitLab From 030b70a2a075c3b29af339d5210a6569e2d14def Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 Apr 2016 11:33:39 +0200 Subject: [PATCH 0304/2403] {vis}[intel-2016a] Pillow 3.2.0 (REVIEW) --- .../Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..bc1187561f --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.2.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('libjpeg-turbo', '1.4.2'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.6.2'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From e53d9aea980e8a51a012176937fea91cb3cf0255 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 6 Apr 2016 15:41:33 +0200 Subject: [PATCH 0305/2403] Libxslt-1.1.28 for foss-2016a --- .../l/libxslt/libxslt-1.1.28-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb new file mode 100644 index 0000000000..63c3fa7e2d --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' \ No newline at end of file -- GitLab From 2f2d57ae191b8c71b2dd9015965a617f608ddb30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 18:01:14 +0200 Subject: [PATCH 0306/2403] consistently use XORG_LIB_SOURCE constant --- easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb | 2 +- .../l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb | 2 +- 34 files changed, 34 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb index bb3839e6a6..ff2702cd71 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.4'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb index 407ce4845d..b63222e9d8 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb index 0fb685525a..1bd7511944 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb index d28d3a6e76..2f28c257c5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb index 0038b41047..bd5ecc8bcd 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb index a15bba69ef..30a7625681 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-intel-2014b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb index 580ce7f28a..a8d0c1fc55 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb index 2a2391d847..c3a28914e6 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb index 641ea44476..503006a89b 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015b.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb index b34ef0db33..1bab5701fe 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb index 3522b7de99..3a034255d6 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X11 client-side library""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.8' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb index 8694ab5ad2..96ec24e1fc 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb index 2e88286d07..934e207665 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-gimkl-2.11.5.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index f1bc2bfb36..bd0254a335 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb index 22bf8016cf..afa4166c18 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb index 408dc4aede..1accebb77f 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb index 9304d0fc79..dafc84e463 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 243dbd6f22..8003dc09d5 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb index 735a0391ab..efb7a8e46c 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2014b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.26'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index c12e65e6e8..20f0072ce3 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb index 9233da540e..395760652d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index cc513f2315..599620e265 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index 79416debdd..0912eb0311 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb index 93de3908f0..1639916a6f 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 24fc239d5e..6ec7ecf45d 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb index 1eeae06c66..b642948a1b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libX11', '1.6.1'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb index 9ce9ef676f..388076a498 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index f5d31320dd..e0c74eaaa7 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb index fea0b330b9..59f66ccd07 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index c076690abe..3b9f118dec 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.27'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb index 23544e2ee3..7c257d0a2f 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b-Python-2.7.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb index 93ffb79a95..3751e0a221 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 3e89327b58..2b4eff3bde 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb index 6f79135801..4646632358 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), -- GitLab From 1e6a202f0f1415b190d434c94c74464ddccbfc9f Mon Sep 17 00:00:00 2001 From: jrbosch Date: Wed, 6 Apr 2016 12:45:43 -0400 Subject: [PATCH 0307/2403] Update libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index bbe5e2fcc0..dcd4997f9b 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ - ('pkg-config', '0.29') + ('pkg-config', '0.29'), ('xproto', '7.0.28'), ] -- GitLab From b9dfd342150f7b28e69e6c96746ab2f2537a5b8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Apr 2016 19:12:21 +0200 Subject: [PATCH 0308/2403] consistently use XORG_*_SOURCE constants --- .../easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb | 2 +- .../easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb | 2 +- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb | 2 +- .../easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb | 2 +- .../easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb | 2 +- easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb | 2 +- .../easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb | 2 +- .../easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb | 2 +- .../easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb | 2 +- .../easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb | 2 +- .../x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb | 2 +- 95 files changed, 95 insertions(+), 95 deletions(-) diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb index 88fa55c14d..1deb262347 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb index 80e72c01e5..574d6d02de 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb index c52db08f49..15154dbbea 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb index 06e3d71fba..4df2be2be9 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb index 5d430a5301..8b11789fca 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb index 3fe841d973..fd373c373a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb index 33951308af..f26ed2df7a 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org FixesProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb index 0719ec51f4..8e577e277b 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb index 6c5ce99387..47f2d3c961 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb index 5c83a62b97..062cfdbcf8 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb index 5b1c1517ba..9c00b32506 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb index f9c5e14a8e..4282ea773f 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb index 06b846c04c..037260e492 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb index 42dc60dd5e..aebc924b14 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb index 8b99a901c9..cb35b32223 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb index 6ccc91bb75..c92de947ba 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb index 2566876879..1f4bad7112 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.16-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb index 46b9bdb324..8a7667c002 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb index 4eb87a66ef..b28bfab5ef 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb index a1f9a0b9d2..191cd512ed 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb index c26a1ac08a..5dd250fddb 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb index 3297e8dea0..ce9480d3aa 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb index 1e1be175b1..475b25485e 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb index 56a7e864e0..7ae3e0efff 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb index 75a9c42cf7..9931bbca58 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb index 804a25ce18..19917b0ef7 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb index e307d5deb4..eb95b2f34a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb index 0437a042db..d652aba387 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb index be4171cde7..cad6b846e6 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb index 1a5db1eefa..b26cb20222 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb index 66fc05b6d4..6a557da522 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb index 21d5d376d5..512fcad715 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb index 83bc32fc03..00ad73c8ec 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb index 323816dd0b..f40968ca7a 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org InputProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb index 7482053f6f..30967e9fe4 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-foss-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb index e54e5f74c9..7e3ad5f572 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb index 3790a57f15..ee1d8ab5ad 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb index 664996727e..48cbc77814 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb index 31cb837d0f..2393fe61dc 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2014b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb index 2d16cb0b13..295d7b8f94 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb index bca5ddd7ca..86f8eb23de 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb index 050b2bda55..a2add0de30 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb index 62923f260f..13dbd2eb08 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb index d692faf393..9a5a48c480 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015b.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb index 29d6a6987a..e5d229774c 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index fc57003279..ce3e6d964e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb index dacbb816a7..3f72d96af4 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb index db2b6fad94..83069f50b6 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-4.1.13.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb index ae82f50061..bd1a547705 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb index 0e5bfb142c..38e0bbe3cc 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb @@ -6,7 +6,7 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb index cb2cc76a3b..87f1456d12 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb index 278cc7bbbf..563fbfcbf2 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = "Xrandr protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb index 3119cd29b7..a354245bf6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb index 48199d0511..9f19fc4dfc 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb index c363620cb6..c2eb005cc6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb index 9d7f0c2a91..c0cb8f56f1 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb index 87042e0e65..59a4298687 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb index b16c201ac1..20a477feb6 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb index 37b516e535..c3ac221b11 100644 --- a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb index 93be023dae..9e6fad7729 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb index 7edd725bb8..6dfd84dd09 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb index 38732656c2..23a639e880 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb index f7d2e42a4b..c294b4f211 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb index 7c6cc82582..4cb4a74155 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """provides bitmaps for x""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] +source_urls = [XORG_DATA_SOURCE] sanity_check_paths = { 'files': ['include/X11/bitmaps/gray'], diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb index 222c1cb8a9..c125fc2989 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb index f8d28a6517..658fd35838 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb index 7e5dd65346..a2085627e9 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb index e73a8f9515..6edad56122 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb index 0f74426405..bd75285755 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb index bceed61321..3876294b7f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb index 9bc6335cdf..53735a84e4 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb index 1800fbf094..beda89b5c6 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index eb7322e162..82aff3127f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb index 6156597f8b..4a87699495 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2014b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb index 96189817b0..91c591e727 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb index d2b93b5852..c2246d9293 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015b.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb index af65fa2a9d..08ca1e412b 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -9,7 +9,7 @@ description = """XExtProto protocol headers.""" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb index b0ee431324..883ec594b7 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb index 797b75e5e7..e582ff06dd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2014b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb index e96e89759a..7e6eb92e97 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2015b.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb index d198aa80e4..892ed9f5bd 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb index f6c2e0c627..572e38002b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index 241268e4a6..6eb06bc7d4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index ab202e5075..5054d70df3 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb index e0f4abf144..ddf767b605 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb index 884e64e8dd..06bdb8bc21 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 8f17ba5d45..7d12c7f86a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb index bdb6d9e8c7..76cc9f4a7a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb index 74b305ce8c..1caa382ace 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index 4ec0e6221a..4d66b00ecb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb index f9bd7118c8..a0292fbf8e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb index 3e787177f0..2a47f2490b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb index 2591e436f9..8dab7213fb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb index d3de936da4..6722798efb 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb index 1d3df458a7..9de353786c 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', -- GitLab From c025b26559a8de6353a6e2f64b8a16413b2f1900 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:06:53 -0500 Subject: [PATCH 0309/2403] Adhering to the 120 characters per line standard for the description variable --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 097d50c5b6..64d81e0783 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Binary" +easyblock = "PackedBinary" name = 'MRIcron' version = '06_22_15' @@ -19,8 +19,8 @@ source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] sources = ['lx.zip'] # Following commands are used to unzip the files and copy the content to install directory -install_cmd = "unzip lx.zip &&" -install_cmd += "cp -a %(builddir)s/* %(installdir)s" +#install_cmd = "unzip lx.zip &&" +#install_cmd += "cp -a %(builddir)s/* %(installdir)s" sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From 8be21fa9d9b4d44c566d83c7b8e48cf187d7f4f5 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:31:56 -0500 Subject: [PATCH 0310/2403] Removing source_url and adding a comment detailing how to download zip'd files manually from the website --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 64d81e0783..a984af8d3b 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,12 +15,10 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://www.nitrc.org/frs/download.php/7765/'] -sources = ['lx.zip'] - -# Following commands are used to unzip the files and copy the content to install directory -#install_cmd = "unzip lx.zip &&" -#install_cmd += "cp -a %(builddir)s/* %(installdir)s" +# Automatic Download doesn't work for this software sice you need to accept their +# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# and place it in a folder where Easybuild can see it. +sources = [SOURCE.ZIP] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d45ee07c957fb86c3a3794ee2ee8f085ccbf68ec Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 13:57:55 -0500 Subject: [PATCH 0311/2403] Corrected some spell errors --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index a984af8d3b..4c0655294e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -15,8 +15,8 @@ Features layers, ROIs, and volume rendering. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -# Automatic Download doesn't work for this software sice you need to accept their -# license, so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ +# Automatic Download doesn't work for this software as you need to accept their license, +# so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. sources = [SOURCE.ZIP] -- GitLab From 4c0b59ae9650f557c12569e0085e22f6ec14e1e2 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 14:34:11 -0500 Subject: [PATCH 0312/2403] Adding the source file to the Easyconfig file --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 4c0655294e..daea20393e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ # and place it in a folder where Easybuild can see it. -sources = [SOURCE.ZIP] +sources = ['lx.zip'] sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], -- GitLab From d97b12f986e603dac7e20078dd6db73d79ac709d Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 6 Apr 2016 15:06:42 -0500 Subject: [PATCH 0313/2403] Adding the md5 checksum value for the source --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index daea20393e..69196eb784 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -20,6 +20,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # and place it in a folder where Easybuild can see it. sources = ['lx.zip'] +checksums = ['a2d8b1c053384220953f6b670d0fd4df'] + sanity_check_paths = { 'files': ["dcm2nii", "dcm2niigui", "mricron", "npm"], 'dirs': ["example", "lut", "templates"] -- GitLab From 29f2c6b09b5e6b7d871d0da26aab6597c5c52163 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:05:56 -0400 Subject: [PATCH 0314/2403] libXrandr-1.5.0 easyconfig for foss-2016a --- .../l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..b6614e79e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libXrandr' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Resize, Rotate and Reflection extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('randrproto', '1.5.0'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrandr.%s' % SHLIB_EXT, 'lib/libXrandr.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a7a61c9d0568c5d4f59df08abb5aae85f3def8f4 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 18:08:32 -0400 Subject: [PATCH 0315/2403] randrproto-1.5.0 easyconfig for foss-2016a --- .../randrproto/randrproto-1.5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000..d480848616 --- /dev/null +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'randrproto' +version = '1.5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrandr protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 44cf756826c8e52b397447b030e627360e7c5bdf Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:38:57 -0400 Subject: [PATCH 0316/2403] libXi-1.7.6 for foss-2016a toolchain --- .../l/libXi/libXi-1.7.6-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb new file mode 100644 index 0000000000..bd92d68db6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a5dd9bfb4552cf157384fbccf9b9538e771453f7 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:39:56 -0400 Subject: [PATCH 0317/2403] libXfixes-5.0.1 for foss-2016a toolchain --- .../l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb new file mode 100644 index 0000000000..aa11951f76 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From fd70a1bdd1a84da2729aa341abe5e8262512e767 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:41:19 -0400 Subject: [PATCH 0318/2403] xorg-macros-1.19.0 for foss-2016a toolchain --- .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 285276c385c90279c966915beba4bb24fbc1aae1 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Wed, 6 Apr 2016 22:44:31 -0400 Subject: [PATCH 0319/2403] fixesproto-5.0 for foss-2016a toolchain --- .../f/fixesproto/fixesproto-5.0-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb new file mode 100644 index 0000000000..b04efa3b3a --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 03e17713072089963a0bceb1a92e343f650ef664 Mon Sep 17 00:00:00 2001 From: "Javier Ruiz Bosch-jrbosch@uclv.cu" Date: Thu, 7 Apr 2016 00:21:05 -0400 Subject: [PATCH 0320/2403] libGLU for foss-2016a toolchain --- .../l/libGLU/libGLU-9.0.0-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb new file mode 100644 index 0000000000..087bd589cb --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '11.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 6db2fe08a4d22e3e21471bca3ae1eb74e3bc437d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 09:37:09 +0200 Subject: [PATCH 0321/2403] use of %(pyver)s --- .../p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb index bc1187561f..e08e25c6bb 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'Pillow' version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://pillow.readthedocs.org/' description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. @@ -12,12 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), -- GitLab From f5cca74c3cae5b9e3e51677a37cc33fd0e25993d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 0322/2403] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 ++++++++++++++- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 ++++++++++++ .../inputproto/inputproto-2.3.1-foss-2016a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.7-foss-2016a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.3-foss-2016a.eb | 37 +++++++++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 34 +++++++++++++++++ .../libXrender/libXrender-0.9.9-foss-2016a.eb | 32 ++++++++++++++++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 ++++++++++++ .../libpthread-stubs-0.3-foss-2016a.eb | 20 ++++++++++ .../l/libxcb/libxcb-1.11.1-foss-2016a.eb | 33 +++++++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++ .../p/PCRE/PCRE-8.38-foss-2016a.eb | 20 ++++++++++ .../renderproto-0.11-foss-2016a.eb | 20 ++++++++++ .../x/xextproto/xextproto-7.3.0-foss-2016a.eb | 24 ++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++ .../x/xproto/xproto-7.0.28-foss-2016a.eb | 23 ++++++++++++ .../x/xtrans/xtrans-1.3.5-foss-2016a.eb | 22 +++++++++++ 18 files changed, 462 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..be4171cde7 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb new file mode 100644 index 0000000000..bca5ddd7ca --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb new file mode 100644 index 0000000000..7bbdcf2dc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb new file mode 100644 index 0000000000..b53c0d9a18 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb new file mode 100644 index 0000000000..12b8caece2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb new file mode 100644 index 0000000000..fcb767cfdb --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb new file mode 100644 index 0000000000..d818b47843 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xevie', '-xf86dri', '-xfixes', + '-xinerama', '-xprint', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb new file mode 100644 index 0000000000..1fe2fcb26c --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb new file mode 100644 index 0000000000..48199d0511 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb new file mode 100644 index 0000000000..9bc6335cdf --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb new file mode 100644 index 0000000000..3e787177f0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb new file mode 100644 index 0000000000..1d32cb1ae6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From f73937858cb1ce3028affcc9f53f79f287f9a3af Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 0323/2403] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 4 ++- .../l/libXau/libXau-1.0.8-foss-2016a.eb | 25 +++++++++++++++++++ .../l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb | 25 +++++++++++++++++++ 3 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..8694ab5ad2 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..c12e65e6e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.28'), +] +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 3f8d502c4b072f4e045c7ed18628e219a304cd24 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:46:56 +0200 Subject: [PATCH 0324/2403] modify easyconfig Blitz++-0.10-foss-2016a.eb, add easyconfig Blitz++-0.10-goolf-1.5.16.eb --- .../b/Blitz++/Blitz++-0.10-foss-2016a.eb | 9 ++------- .../b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 20 +++++++++++++++++++ 2 files changed, 22 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index 03886c8db9..f91bad5dd3 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -10,16 +10,11 @@ description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array toolchain = {'name': 'foss', 'version': '2016a'} sources = ['blitz-%(version)s.tar.gz'] -source_urls = ['https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', - 'download'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] sanity_check_paths = { 'files': ['lib/libblitz.a'], - 'dirs': ['include/blitz/array', - 'include/blitz/gnu', - 'include/blitz/meta', - 'include/random', - 'lib/pkgconfig'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb new file mode 100644 index 0000000000..f75014e6f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' +description = """Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ + with a speed comparable to Fortran implementations, while preserving an object-oriented interface""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +sources = ['blitz-%(version)s.tar.gz'] +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 9f9d4d40dcff4c9109de8ce909ca0e950a386531 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:53:06 +0200 Subject: [PATCH 0325/2403] modify easyconfig Saxon-HE-9.7.0.4-Java-1.7.0_79.eb --- .../easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index eed56a9078..d38576ab53 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'Saxon-HE' version = '9.7.0.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://saxon.sourceforge.net' description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" @@ -9,11 +10,8 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] - source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] -versionsuffix = '-Java-%(javaver)s' - dependencies = [('Java', '1.7.0_79')] jarfiles = ['saxon%(version_major)she.jar', 'saxon%(version_major)s-test.jar', 'saxon%(version_major)s-xqj.jar'] -- GitLab From 4c3641259118bc70d74b75893f2c24e348a1d661 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 Apr 2016 11:40:45 +0200 Subject: [PATCH 0326/2403] 1 --- .../g/GConf/GConf-3.2.6-intel-2016a.eb | 39 ++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 45 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb new file mode 100644 index 0000000000..118e97695c --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('libxml', '2.9.3'), + ('GTK+', '2.24.28'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb new file mode 100644 index 0000000000..2bca75979e --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -0,0 +1,45 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('expat', '2.1.0'), + ('GTK+', '2.24.28'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/wxrc'] + + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + + ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], + 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], +} + +moduleclass = 'vis' -- GitLab From fb1feec5cb73661660cfa839cf2ff6aa193a2b5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 7 Apr 2016 15:42:40 +0200 Subject: [PATCH 0327/2403] removed newline --- easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb index 63c3fa7e2d..6b593148b4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -21,4 +21,4 @@ dependencies = [ ('libxml2', '2.9.3'), ] -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' -- GitLab From 7b27041bb0c383832ffb63e6f205c1f091a3934a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 15:59:16 +0200 Subject: [PATCH 0328/2403] add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb --- .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From 690b3dbdd43db476033b8e56facd240268975327 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 16:45:13 +0200 Subject: [PATCH 0329/2403] add easyconfig MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb, add easyconfig libxml2-2.9.2-goolf-1.5.16.eb, add easyconfig HDF5-1.8.9-goolf-1.5.16.eb, add easyconfig Szip-2.1-goolf-1.5.16.eb --- .../h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 22 ++++++++++++++ .../l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 29 ++++++++++++++++++ ...goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 30 +++++++++++++++++++ .../s/Szip/Szip-2.1-goolf-1.5.16.eb | 23 ++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..755c2cc7f9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 +name = 'HDF5' +version = '1.8.9' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..54c5dad803 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb new file mode 100644 index 0000000000..a5aa488ebe --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.0.67' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.','-')] + +dependencies = [ + ('Java', '1.7.0_79', '', True), + ('Python', '2.7.9'), + ('HDF5', '1.8.9'), + ('libxml2', '2.9.2'), + ('zlib', '1.2.8') +] + +configopts = '--with-jdk=$JAVA_HOME' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..73e27f5f6c --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolf-1.5.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 55bbb83dc4b022930eb235f433ce199dc864a355 Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 7 Apr 2016 18:53:44 +0200 Subject: [PATCH 0330/2403] updated to only use one version of CMake and fixed remarks --- .../CMake-3.5.0-CrayGNU-2015.11.eb} | 9 +++---- .../d/DCA/DCA++-CMake-CrayGNU-2015.11.eb | 3 ++- .../g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb | 26 ------------------- .../easyconfigs/m/magma/magma-2.0.0.patch | 6 ++--- 4 files changed, 9 insertions(+), 35 deletions(-) rename easybuild/easyconfigs/c/{cmake/CMake-3.3.1-CrayGNU-2015.11.eb => CMake/CMake-3.5.0-CrayGNU-2015.11.eb} (74%) diff --git a/easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb similarity index 74% rename from easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb index 0fd1f3f091..fc32d0f617 100644 --- a/easybuild/easyconfigs/c/cmake/CMake-3.3.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -1,24 +1,23 @@ -# Built with EasyBuild version 2.5.0 on 2016-01-22_09-06-09 +# Contributed by Luca Marsella (CSCS) easyblock = 'ConfigureMake' name = 'CMake' -version = "3.3.1" +version = '3.5.0' homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'dynamic': True} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '6.0', '', True)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb b/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb index a03ec7b4ae..7d57829763 100644 --- a/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'DCA++' version = '1.0' +versionsuffix = '-cuda' #consider building everything with eb: #preinstallopts: change build_directory @@ -13,7 +14,7 @@ description = """This modules bundles all the dependencies for DCA++, the best D toolchain = {'name': 'CrayGNU', 'version': '2015.11'} dependencies = [ - ('CMake', '3.3.1'), + ('CMake', '3.5.0'), ('spglib', '1.7.3'), ('NFFT', '3.3.0'), ('magma', '2.0.0'), diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb index 0942442516..3ebc1003fc 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.5.0 on 2016-01-22_09-08-42 easyblock = "Tarball" name = 'gtest' @@ -18,28 +17,3 @@ sanity_check_paths={ } moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.5.0", - "easybuild-easyblocks_version": "2.5.0", - "timestamp": 1453450122, - "build_time": 3.29, - "install_size": 5091756, - "command_line": ['--buildpath=/dev/shm/haehneru', '--experimental', '--external-modules-metadata=cray-netcdf/4.3.2,cray-hdf5/1.8.13,cray-hdf5-parallel/1.8.13,cray-libsci/13.0.4,cray-libsci/13.2.0,cudatoolkit/6.5.14-1.0502.9613.6.1,cudatoolkit/6.5.14-1.0502.9836.8.1,cudatoolkit/7.0.28-1.0502.10742.5.1,cray-petsc-complex-64/3.5.3.1,cray-petsc-complex/3.5.3.1,cray-petsc/3.5.3.1,cray-petsc-64/3.5.3.1,gcc/4.9.2', '--group-writable-installdir', '--hide-deps=Bison,Doxygen,JasPer,NASM,SQLite,Szip,Tcl,bzip2,cURL,flex,freetype,libjpeg-turbo,libpng,libreadline,libtool,libxml2,ncurses,zlib,M4,Serf,APR,APR-util,expat,SCons', '--installpath=/project/s299/easybuild/daint/easybuild', '--optarch=sandybridge', '--packagepath=/project/s299/easybuild/daint/easybuild/packages', '--prefix=/project/s299/easybuild/daint/easybuild', '--repositorypath=/project/s299/easybuild/daint/easybuild/ebfiles_repo/', '--robot=/apps/common/easybuild/cscs_easyconfigs/:/apps/common/easybuild/ebfiles_repo/daint:/apps/common/UES/easybuild/software/EasyBuild/2.5.0/lib64/python2.6/site-packages/easybuild_easyconfigs-2.5.0-py2.6.egg/easybuild/easyconfigs', '--robot-paths=/apps/common/easybuild/cscs_easyconfigs/:/apps/common/easybuild/ebfiles_repo/daint:', '--set-gid-bit', '--sourcepath=/users/haehneru', '--umask=002', 'DCA++-CMake-CrayGNU-2015.06-XC.eb'], - "modules_tool": ('EnvironmentModulesC', '/opt/modules/3.2.10.3/bin/modulecmd', '3.2.10'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2599.904, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/opt/gcc/4.8.2/bin/../snos/bin/gcc; COLLECT_LTO_WRAPPER=/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/lto-wrapper; Target: x86_64-suse-linux; Configured with: ../cray-gcc-4.8.2/configure --prefix=/opt/gcc/4.8.2/snos --disable-nls --libdir=/opt/gcc/4.8.2/snos/lib --enable-languages=c,c++,fortran --with-gxx-include-dir=/opt/gcc/4.8.2/snos/include/g++ --with-slibdir=/opt/gcc/4.8.2/snos/lib --with-system-zlib --enable-shared --enable-__cxa_atexit --build=x86_64-suse-linux --with-mpc=/opt/gcc/mpc/0.8.1 --with-mpfr=/opt/gcc/mpfr/2.4.2 --with-gmp=/opt/gcc/gmp/4.3.2; Thread model: posix; gcc version 4.8.2 20131016 (Cray Inc.) (GCC) ; ", - "glibc_version": "2.11.3", - "hostname": "daint103", - "os_name": "SLES", - "os_type": "Linux", - "os_version": "11_SP3", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.9 (unknown, Apr 7 2015, 08:28:12) ; [GCC 4.3.4 [gcc-4_3-branch revision 152973]]", - "system_gcc_path": "/opt/gcc/4.8.2/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch index 1f81da8c77..ca07f75ad2 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch @@ -45,11 +45,11 @@ diff -ru magma-2.0.0.orig//make.inc.openblas magma-2.0.0/make.inc.openblas - -CC = gcc -CXX = g++ -+CXX = CC -+CC = cc ++#CXX = $(CXX) ++#CC = $(CC) NVCC = nvcc -FORT = gfortran -+FORT = ftn ++FORT = $(F90) ARCH = ar ARCHFLAGS = cr -- GitLab From 07c13c35a15245cc7f1e9ce02a87d17299bee0ae Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 7 Apr 2016 18:57:02 +0200 Subject: [PATCH 0331/2403] move to ncurses 5.9 to match with existing version on the repo --- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb index fc32d0f617..5805e83d42 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('ncurses', '6.0', '', True)] +dependencies = [('ncurses', '5.9', '', True)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From 680678003bfaa4338c9b181d6da9ad29ce31540a Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 7 Apr 2016 18:58:14 +0200 Subject: [PATCH 0332/2403] minor fix --- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb index 5805e83d42..c7cd4a579a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('ncurses', '5.9', '', True)] +dependencies = [('ncurses', '5.9')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From 59936412cadec6214dff63e5467125fe8c32f1a5 Mon Sep 17 00:00:00 2001 From: perettig Date: Thu, 7 Apr 2016 19:00:57 +0200 Subject: [PATCH 0333/2403] minor --- easybuild/easyconfigs/m/magma/magma-2.0.0.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch index ca07f75ad2..449bdbd78d 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch @@ -45,8 +45,8 @@ diff -ru magma-2.0.0.orig//make.inc.openblas magma-2.0.0/make.inc.openblas - -CC = gcc -CXX = g++ -+#CXX = $(CXX) -+#CC = $(CC) ++#CXX = CC # Variable already defined by EasyBuild ++#CC = cc # Variable already defined by EasyBuild NVCC = nvcc -FORT = gfortran +FORT = $(F90) -- GitLab From ec8c9fd7d0dadd4dd1c5089f6135a0e87a76e244 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 8 Apr 2016 09:26:38 +0200 Subject: [PATCH 0334/2403] add easyconfig Python-2.7.9-goolf-1.5.16.eb, add easyconfig bzip2-1.0.6-goolf-1.5.16.eb, add easyconfig libreadline-6.3-goolf-1.5.16.eb, add easyconfig ncurses-5.9-goolf-1.5.16.eb, add easyconfig SQLite-3.8.8.1-goolf-1.5.16.eb, add easyconfig Tk-8.6.3-goolf-1.5.16-no-X11.eb, add easyconfig OpenSSL-1.0.1k-goolf-1.5.16.eb --- .../b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb | 15 +++ .../libreadline-6.3-goolf-1.5.16.eb | 30 +++++ .../n/ncurses/ncurses-5.9-goolf-1.5.16.eb | 36 ++++++ .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb | 24 ++++ .../p/Python/Python-2.7.9-goolf-1.5.16.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb | 38 ++++++ .../t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb | 25 ++++ 7 files changed, 284 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb new file mode 100644 index 0000000000..1f608a116f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..9a2a57c200 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..0d4841191f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.16.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb new file mode 100644 index 0000000000..895b5bd87b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1k' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb new file mode 100644 index 0000000000..dee7cd4fdf --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), + ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..6946daaee7 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb new file mode 100644 index 0000000000..b383831c92 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2b8706a0b067912224fda3a480f910701fe0cbe4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Mar 2016 17:19:45 +0200 Subject: [PATCH 0335/2403] add easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig freetype-2.6.2-foss-2016a.eb, add easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig pixman-0.34.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 29 +++++++++++++++++++ .../f/freetype/freetype-2.6.2-foss-2016a.eb | 3 +- .../p/pixman/pixman-0.34.0-foss-2016a.eb | 20 +++++++++++++ 3 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb new file mode 100644 index 0000000000..4afe79dcce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.2'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 41c2f0204e..3111a314be 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -14,8 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, - 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb new file mode 100644 index 0000000000..896aab1550 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 2fb7134c01aa47664c480fb407f7242b41013d51 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 03:45:51 -0400 Subject: [PATCH 0336/2403] support for Yade but it's not yet completed --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb new file mode 100644 index 0000000000..3711be5fc1 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -0,0 +1,88 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' + +homepage = 'www.yade-dem.org' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('git', '2.8.0'), + ('freeglut', '3.0.0'), + ('loki', '-------'), + ('Boost', '1.60.0'), + ('fakeroot', '-------'), + ('dpkg', '-------'), + ('IPython', '3.2.3', versionsuffix), + ('matplotlib', '1.5.1'), + ('SQLite', '3.9.2'), + ('numpy', '1.10.4', versionsuffix) + ('TK', '8.6.4', 'no-X11'), + ('gnuplot', '5.0.3'), + ('gts', '0.7.6'), + ('Graphviz', '2.38'), + ('ScientificPython', '2.9.4', versionsuffix), + ('Eigen', '3.2.7'), + ('Qt', '4.8.7'), + ('gtk+', '2.24.28'), + ('libqglviewer-dev', '-------'), + ('libjs-jquery', '---------'), + ('Sphinx', '1.3.3'), + ('bibtexparser', '0.6.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6'), + ('help2man', '--------'), + ('bzip2', '1.0.6'), + ('ziblg-dev', '---------------'), + ('GDB', '7.10.1',versionsuffix), + # optional + ('VTK', '6.3.0'), + ('CGAL', '4.7'), + ('SuiteSparse', '4.5.1'), + ('OpenBLAS', '0.2.15'), + ('METIS', '5.1.0'), +] + +builddependencies = [('CMake', '3.2.3')] + +separate_build_dir = True + +# In case you want disable some Yade features +# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' + +# options available, +# ENABLE_GUI: enable GUI option (ON by default) +# ENABLE_CGAL: enable CGAL option (ON by default) +# ENABLE_VTK: enable VTK-export option (ON by default) +# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) +# ENABLE_GTS: enable GTS-option (ON by default) +# ENABLE_GL2PS: enable GL2PS-option (ON by default) +# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) +# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) +# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) +# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) +# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) +# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) +# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) +# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) +# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) +# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) +# USE_QT5: use QT5 for GUI, experimental (OFF by default) + +sanity_check_paths = { + 'files': ['bin/%s-%s' %(namelower, version), 'bin/%s-%s-batch' %(namelower, version)], + 'dirs': ['lib/x86_64-linux-gnu'] +} + +moduleclass = 'devel' -- GitLab From 821479d0f1049f642b3f2ff7cfb9a2fca8f9206b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:18:48 +0200 Subject: [PATCH 0337/2403] 2 --- .../d/DBus/DBus-1.10.8-intel-2016a.eb | 24 +++++++++++ .../dbus-glib/dbus-glib-0.106-intel-2016a.eb | 25 +++++++++++ .../g/GConf/GConf-3.2.6-intel-2016a.eb | 5 ++- .../GST-plugins-base-0.10.36-intel-2016a.eb | 37 +++++++++++++++++ .../GStreamer-0.10.36-intel-2016a.eb | 41 +++++++++++++++++++ ...intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 25 +++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 6 +++ ...XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb | 27 ++++++++++++ 8 files changed, 188 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb new file mode 100644 index 0000000000..f322881382 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb new file mode 100644 index 0000000000..321204b244 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('DBus', '1.10.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index 118e97695c..ec87efba55 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -8,7 +8,7 @@ description = """GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.""" -toolchain = {'name': 'intel', 'version': '2014b'} +toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] @@ -17,8 +17,9 @@ dependencies = [ ('dbus-glib', '0.106'), ('GLib', '2.47.5'), ('GObject-Introspection', '1.47.1'), - ('libxml', '2.9.3'), + ('libxml2', '2.9.3'), ('GTK+', '2.24.28'), + ('intltool', '0.51.0', '-Perl-5.22.1'), ] configopts = '--disable-orbit ' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..914e875639 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb new file mode 100644 index 0000000000..6c81f735d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.47.5'), + ('GObject-Introspection', '1.47.1'), + ('zlib', '1.2.8'), +] + +#Does not work with Bison 3 +builddependencies = [ +# ('Bison', '2.7', '', True), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..4c3bc089de --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 2bca75979e..439291d7b0 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,3 +1,6 @@ +easyblock = 'ConfigureMake' +#easyblock = 'PythonPackage' + name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -31,6 +34,9 @@ dependencies = [ parallel = 1 +#options = {'modulename': 'wx'} +#skipsteps = ['install_step', 'make_installdir' ] + sanity_check_paths = { 'files': ['bin/wxrc'] + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..5cb19baa1c --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-intel-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From 0263a7c1eae14b20cf0d549b928a77037cdc15ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:39:37 +0200 Subject: [PATCH 0338/2403] Builddependencies fixed for GObject-introspection --- .../GObject-Introspection-1.42.0-intel-2014b.eb | 4 +++- .../GObject-Introspection-1.44.0-intel-2015a.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2015b.eb | 3 +++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 8 +++++--- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb index 7ae4e4f769..1f246a9bfc 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -18,9 +18,11 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.8'), ('GLib', '2.40.0'), - ('Bison', '3.0.2'), ] +builddependencies = [ + ('Bison', '3.0.2'), +] sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb index 0461a34f5f..835de46b5b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.44.1'), +] + +builddependencies = [ ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 7bff362648..3e1f37f646 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,6 +18,9 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), +] + +builddependencies = [ ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index eaa343080d..360f641464 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From 7b8ff1272ac3332e3a75cb50cf751cb568ae4ea2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 10:44:38 +0200 Subject: [PATCH 0339/2403] fixed gobject-intro builddep --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 3c83530c29..2ea4584a28 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -20,14 +20,16 @@ pyver = '2.7.11' dependencies = [ ('Python', pyver), ('GLib', '2.47.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), ('flex', '2.6.0'), ('Bison', '3.0.4'), ('cairo', '1.14.6'), - ('libffi', '3.2.1'), ] -builddependencies = [('Autotools', '20150215')] - preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts -- GitLab From ab78bd9b77913e4fc297e3a80c01225d559b051b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:02:48 +0200 Subject: [PATCH 0340/2403] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig GLib-2.47.5-foss-2016a.eb, modify easyconfig freetype-2.6.2-foss-2016a.eb, modify easyconfig pixman-0.34.0-foss-2016a.eb, modify easyconfig fontconfig-2.11.94-foss-2016a.eb, add easyconfig libX11-1.6.3-foss-2016a.eb, add easyconfig libxcb-1.11.1-foss-2016a.eb, add easyconfig libXrender-0.9.9-foss-2016a.eb, add easyconfig libXext-1.3.3-foss-2016a.eb, add easyconfig renderproto-0.11-foss-2016a.eb, add easyconfig xextproto-7.3.0-foss-2016a.eb, add easyconfig xproto-7.0.28-foss-2016a.eb, add easyconfig libffi-3.2.1-foss-2016a.eb, add easyconfig gettext-0.19.7-foss-2016a.eb, add easyconfig libxml2-2.9.3-foss-2016a-Python-2.7.11.eb, add easyconfig PCRE-8.38-foss-2016a.eb, add easyconfig inputproto-2.3.1-foss-2016a.eb, add easyconfig libpthread-stubs-0.3-foss-2016a.eb, add easyconfig kbproto-1.0.7-foss-2016a.eb, add easyconfig xtrans-1.3.5-foss-2016a.eb, add easyconfig xorg-macros-1.19.0-foss-2016a.eb --- .../c/cairo/cairo-1.14.6-foss-2016a.eb | 30 +++++++++++++++-- .../g/GLib/GLib-2.47.5-foss-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../l/libXext/libXext-1.3.3-foss-2016a.eb | 1 + .../libXrender/libXrender-0.9.9-foss-2016a.eb | 4 +++ .../l/libffi/libffi-3.2.1-foss-2016a.eb | 23 +++++++++++++ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++ .../xorg-macros-1.19.0-foss-2016a.eb | 22 +++++++++++++ 8 files changed, 164 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index 4afe79dcce..ab395e2001 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = "cairo" +name = 'cairo' version = '1.14.6' homepage = 'http://cairographics.org' @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] +glibver = '2.47.5' + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), @@ -21,9 +23,33 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.94'), ('expat', '2.1.0'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), +] + +builddependencies = [ + ('renderproto', '0.11'), + ('libXext', '1.3.3'), + ('xextproto', '7.3.0'), + ('libX11', '1.6.3'), + ('xproto', '7.0.28'), + ('libxcb', '1.11.1') ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no" +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb new file mode 100644 index 0000000000..fb0fcbff8c --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.47.5-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.47.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index ce3e6d964e..0a0acbe42b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..12b8caece2 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,10 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libX11', '1.6.3'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb new file mode 100644 index 0000000000..c7c638b6fa --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0237c8f83b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +pythonver = '2.7.11' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb new file mode 100644 index 0000000000..3965c12078 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.0' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 23d49b344a3159cf6e1b84a0e873754b08789e41 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 7 Apr 2016 10:21:22 +0200 Subject: [PATCH 0341/2403] modify easyconfig cairo-1.14.6-foss-2016a.eb, add easyconfig libXau-1.0.8-foss-2016a.eb, add easyconfig libXdmcp-1.1.2-foss-2016a.eb --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb index ab395e2001..5cf49b60d8 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a.eb @@ -25,9 +25,11 @@ dependencies = [ ('expat', '2.1.0'), ('GLib', glibver), ('libX11', '1.6.3'), + ('libXau', '1.0.8'), ('libxcb', '1.11.1'), - ('libXrender', '0.9.9'), + ('libXdmcp', '1.1.2'), ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), ] builddependencies = [ -- GitLab From 3dcbdd98222ef584623e17fe698cf4f602897cdc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 8 Apr 2016 12:02:01 +0100 Subject: [PATCH 0342/2403] Update IGVTools to 2.3.72 --- .../IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb new file mode 100644 index 0000000000..af0616b491 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.72' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4dab0a4ea3bcc8e35b8f22daab6ba0ebe764a781 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 8 Apr 2016 14:42:42 +0200 Subject: [PATCH 0343/2403] {vis}[intel-2016a] wxPython 3.0.2.0 (REVIEW) --- .../GST-plugins-base-0.10.36-intel-2016a.eb | 4 +-- .../GStreamer-0.10.36-intel-2016a.eb | 4 +-- .../libXxf86vm-1.1.4-intel-2016a.eb | 30 +++++++++++++++++++ ...Python-3.0.2.0-intel-2016-Python-2.7.11.eb | 12 ++++---- .../w/wxPython/wxPython_3.0.2.0_intel.patch | 12 ++++++++ .../xf86vidmodeproto-2.3.1-intel-2016a.eb | 19 ++++++++++++ 6 files changed, 69 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch create mode 100644 easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 914e875639..af962689d7 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -18,9 +18,7 @@ dependencies = [('GStreamer', '0.10.36')] #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 6c81f735d4..178e012daf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -22,9 +22,7 @@ dependencies = [ #Does not work with Bison 3 builddependencies = [ -# ('Bison', '2.7', '', True), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), + ('Bison', '2.7', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..873ae3da80 --- /dev/null +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXxf86vm' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xf86vidmodeproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vmode.h']+ + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 439291d7b0..4d7ba463bd 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -1,6 +1,3 @@ -easyblock = 'ConfigureMake' -#easyblock = 'PythonPackage' - name = 'wxPython' version = '3.0.2.0' versionsuffix = "-Python-%(pyver)s" @@ -30,12 +27,15 @@ dependencies = [ ('GTK+', '2.24.28'), ('GConf', '3.2.6'), ('GST-plugins-base', '0.10.36'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('libSM', '1.2.2'), + ('libXxf86vm', '1.1.4'), ] -parallel = 1 +options = {'modulename': 'wx'} -#options = {'modulename': 'wx'} -#skipsteps = ['install_step', 'make_installdir' ] +parallel = 1 sanity_check_paths = { 'files': ['bin/wxrc'] + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch new file mode 100644 index 0000000000..ac58f0c1ac --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.2.0_intel.patch @@ -0,0 +1,12 @@ +# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) +# B. Hajgato (VUB) April 8th 2016 +--- wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py.org 2014-11-27 21:49:59.000000000 +0100 ++++ wxPython-src-3.0.2.0/build/tools/build-wxwidgets.py 2016-04-08 13:03:01.362591062 +0200 +@@ -268,6 +268,7 @@ + configure_opts.append("--with-gtk=3") + + wxpy_configure_opts = [ ++ "--disable-precomp-headers", + "--with-opengl", + "--enable-sound", + "--enable-graphics_ctx", diff --git a/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb new file mode 100644 index 0000000000..3665e42444 --- /dev/null +++ b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xf86vidmodeproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vm%s.h' % x for x in ['', 'proto', 'str']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 556b6294cd2ae5229d67cc4986caa48b4a0bcb33 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 15:52:14 -0400 Subject: [PATCH 0344/2403] add ScientificPython 2.9.4 and numpy 1.10.4 for foss 2016a toolchain --- .../numpy-1.10.4-foss-2016a-Python-2.7.11.eb | 26 ++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f2c859648a --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a597bd3eff --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'ScientificPython' +version = '2.9.4' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.10.4', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 2f44609dc27711bf4292e2b9101d2cbac77061f1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 8 Apr 2016 16:38:14 -0400 Subject: [PATCH 0345/2403] Update source_urls parameter in ScientificPython easyconfig files --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 +- .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 +- .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..c1aca8b5ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'gmpolf', 'version': '1.4.8'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..65204949fb 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..25d50d354e 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ and parallelization.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..9274b5b9ad 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..5aa3dd118d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.2.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..89a12d0943 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/2309'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..b745e7f0a4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4411'] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..876a244102 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..857fd95a08 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -10,7 +10,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] pyver = '2.7.11' -- GitLab From c74b00de25ab3199f39cde3c889c01383f1ef871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 11:21:50 +0200 Subject: [PATCH 0346/2403] use XORG_LIB_SOURCE everywhere --- easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb index fa49f6c97c..78420c88a5 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -9,7 +9,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb index fe3df1bbcf..289966eec9 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -10,7 +10,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.9'), -- GitLab From 1a9927879a743d52c447108463b62b095a6d15ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 12:19:03 +0200 Subject: [PATCH 0347/2403] add checksums in SuiteSparse easyconfigs --- .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb | 2 ++ .../ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb | 2 ++ .../ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb | 2 ++ 9 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb index b783e38692..ce094bf25b 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f3c253971b..a89c80a516 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb index ed6a708c5f..51bacf787c 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-goolf-1.4.10-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb index 20336396df..a889a4de4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-4.0.6-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb index fcc68a81ed..2c70b32004 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.2.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.2.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb index 997b8a1673..e0938abda4 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-ictce-5.3.0-Python-2.7.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['82d8592635d6ae8608b3073dacf9e694'] + python = "Python" pythonversion = '2.7.3' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb index 2446abe86f..feb8f56c9d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8.1-intel-2014b-Python-2.7.8.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/2309'] sources = [SOURCE_TAR_GZ] +checksums = ['73ee0df19c7b58cdf2954261f0763c77'] + python = "Python" pythonversion = '2.7.8' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb index 0170615e9c..01aca5b107 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + python = 'Python' pythonversion = '2.7.9' pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb index 47671f1164..20da6ee305 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015b-Python-2.7.11.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] sources = [SOURCE_TAR_GZ] +checksums = ['dc2987089e106cb807b4ccecf7adc071'] + pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -- GitLab From ff6955fedb6d0c154f4ab0b3d8f057f986c215d7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 12:10:39 +0100 Subject: [PATCH 0348/2403] Initial version of bam-readcount --- ...readcount-0.7.4-cmake_install_prefix.patch | 12 +++++++ .../bam-readcount-0.7.4-foss-2015b.eb | 35 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch new file mode 100644 index 0000000000..2916d1f5e7 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -0,0 +1,12 @@ +diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt +--- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 ++++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 +@@ -2,7 +2,7 @@ + + project(bam-readcount) + +-set(CMAKE_INSTALL_PREFIX "/usr") ++#set(CMAKE_INSTALL_PREFIX "/usr") + set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake;${CMAKE_SOURCE_DIR}/build-common/cmake") + include(TestHelper) + include(VersionHelper) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb new file mode 100644 index 0000000000..b19ba9482c --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.7.4' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/genome/%(name)s/archive'] + +patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] + +builddependencies = [ + ('SAMtools', '1.3'), + ('CMake', '3.4.1'), +] + +configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 09e71b456c69f7db1a62915a145b1dab23b5e952 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 15:21:46 +0200 Subject: [PATCH 0349/2403] use XORG_PROTO_SOURCE + 'env' in preconfigopts --- .../easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb | 2 +- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb index 0d7fd4a4a2..1fbffb2758 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb index d26077ac1e..850097aee1 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index 75924f159f..c39482e40c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " +preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index c9dd66c1c1..fb2151e5df 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -53,7 +53,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float " #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' -prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, -- GitLab From 68db97d838656d94d12133f292533dc2670c42f0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 9 Apr 2016 14:51:56 +0100 Subject: [PATCH 0350/2403] Remove obsolete configopts and add explanation/authorship to patch --- .../bam-readcount-0.7.4-cmake_install_prefix.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch index 2916d1f5e7..aecba22db8 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch @@ -1,3 +1,7 @@ +# patch to remove hard-coded installation prefix +# Adam Huffman +# The Francis Crick Institute + diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt --- bam-readcount-0.7.4/CMakeLists.txt 2014-12-07 19:45:03.000000000 +0000 +++ bam-readcount-0.7.4.new/CMakeLists.txt 2016-04-06 22:06:12.336807391 +0100 -- GitLab From 86e08e86be0bf0b7717a15b4bd15b9ace3b60c60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:37:07 +0200 Subject: [PATCH 0351/2403] sync preconfigopts/buildopts in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 5 +++++ .../GObject-Introspection-1.47.1-intel-2016a.eb | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 3e1f37f646..42f9c4f97f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -24,6 +24,11 @@ builddependencies = [ ('Bison', '3.0.4'), ] +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index 360f641464..7606731e75 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -30,7 +30,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -- GitLab From ebb1e4c1d3f91f420161ddacb12c4270b9380e84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 16:39:35 +0200 Subject: [PATCH 0352/2403] sync (build) deps in GObject-Introspection 1.47.1 easyconfigs --- .../GObject-Introspection-1.47.1-intel-2015b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb index 42f9c4f97f..b1d634cd35 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2015b.eb @@ -18,10 +18,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), ('GLib', '2.47.1'), + ('libffi', '3.2.1'), ] builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('cairo', '1.14.4'), ] preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " -- GitLab From d0eedfe69ed10024cd995cb170fddb0d1467732d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 17:27:10 +0200 Subject: [PATCH 0353/2403] various small style fixes --- .../GObject-Introspection-1.47.1-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 1 + .../l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb | 1 + easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb | 1 + .../m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb | 2 +- .../m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb | 2 +- .../m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb | 2 +- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015a.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2015b.eb | 2 +- .../m/makedepend/makedepend-1.0.5-intel-2016a.eb | 2 +- 19 files changed, 20 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index 2ea4584a28..ef2d0a1446 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -15,10 +15,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -pyver = '2.7.11' - dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ('GLib', '2.47.5'), ('libffi', '3.2.1'), ] @@ -30,7 +28,7 @@ builddependencies = [ ('cairo', '1.14.6'), ] -preconfigopts = "GI_SCANNER_DISABLE_CACHE=true " +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 6943d3e084..68589245d1 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb index eaa232fe89..cd973d2ea0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b-Python-2.7.11.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' versionsuffix = '-Python-2.7.11' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 0ed8e42a20..60cd626d31 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.4' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index bd92d68db6..c94df236e0 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 265985f5e5..5e9d4cb87a 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'libXi' version = '1.7.6' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb index 3b30e0e1d5..6fb02db3e5 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb index 393090c994..00c6dd2232 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb index f5f634beae..82ed5ca658 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-3.2.2.u3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb index 25ba8c0849..c4b315a1b7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb index 858f7c2608..255cd2ad52 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb index 808282ac91..49f692fd43 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb index 873b6391a2..ece06f94eb 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb index 07b6b524bf..50e1707937 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.4-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] patches = ['makedepend_icc-sigaction.patch'] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 8bd95eee91..863911703e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index c92d8634e2..38d76d37d2 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 0b36b37c50..282179280a 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index 77541afc67..ca6025105b 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index 1158bd68be..e38d07d26e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From 25115093469d2add35217998147dd08a68ce16aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 18:34:13 +0200 Subject: [PATCH 0354/2403] use XORG_PROTO_SOURCE --- .../x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb index a40280e419..fdbb9a1f7d 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -9,7 +9,7 @@ description = "X protocol and ancillary headers for xinerama" toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], -- GitLab From 6e3de4adfa74be7ef5b164931fa37c5dba22be68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:23:28 +0200 Subject: [PATCH 0355/2403] clean up wxPython easyconfig according to enhancements to wxPython easyblock --- .../wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb index 4d7ba463bd..803388b88a 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb @@ -33,19 +33,4 @@ dependencies = [ ('libXxf86vm', '1.1.4'), ] -options = {'modulename': 'wx'} - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/wxrc'] + - ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + - ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], - 'dirs': ['include', 'share', 'lib/python%(pyshortver)s/site-packages'] -} - -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/wx-3.0-gtk2'], -} - moduleclass = 'vis' -- GitLab From 71405555deacf3b3a4280055e2b11d53317629f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Apr 2016 20:35:55 +0200 Subject: [PATCH 0356/2403] style fixes --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 1 - .../GST-plugins-base-0.10.36-intel-2016a.eb | 6 +++--- .../g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 9 +++++---- .../intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index ec87efba55..89fe1cefe2 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index af962689d7..f2d1e756a5 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -16,14 +16,14 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [('GStreamer', '0.10.36')] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + - ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 178e012daf..ccd3a73617 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -20,15 +20,16 @@ dependencies = [ ('zlib', '1.2.8'), ] -#Does not work with Bison 3 +# does not work with Bison 3.x builddependencies = [ ('Bison', '2.7', '', True), ] sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], - 'dirs': ['include', 'share', 'libexec'] + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], } modextrapaths = { diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb index 4c3bc089de..0b9db08cff 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ -- GitLab From 9fe4ba351aca7af665bb92fb5ce3a5220bb630a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Apr 2016 10:47:20 +0200 Subject: [PATCH 0357/2403] fix typo in filename for wxPython --- ...on-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/wxPython/{wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb => wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016-Python-2.7.11.eb rename to easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb -- GitLab From 8ac5aefb82cd2237cd679ba3c103e973ee3f9581 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 10 Apr 2016 16:00:31 +0200 Subject: [PATCH 0358/2403] Fix build/runtime dependencies --- .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index 12b8caece2..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,7 +14,6 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), - ('libX11', '1.6.3'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28') -- GitLab From 75e2d85779aa974e7c506e0a95547fa6618ddc73 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 21:26:14 +0100 Subject: [PATCH 0359/2403] Really remove the obsolete configopts this time --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index b19ba9482c..a786a5b208 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -21,8 +21,6 @@ builddependencies = [ ('CMake', '3.4.1'), ] -configopts = " -DCMAKE_INSTALL_PREFIX=%(installdir)s " - prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From e3800389846428f835f7674d1e3a9d31923189c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:17:21 +0100 Subject: [PATCH 0360/2403] Port GROMACS 5.1.2 to foss-2016a --- .../GROMACS-5.1.2-foss-2016a-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb new file mode 100644 index 0000000000..5b189abdbd --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.4.1'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 0382afb4bd7cb2f5c50dd5364d7090eb238747df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 10 Apr 2016 23:50:25 +0100 Subject: [PATCH 0361/2403] Update libxml2 to 2.9.3 for foss-2016a --- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb index 5b189abdbd..e699b7dd9b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -31,7 +31,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.4.1'), - ('libxml2', '2.9.2') + ('libxml2', '2.9.3') ] dependencies = [('Boost', '1.60.0')] -- GitLab From 22adb35c727a98b0064b959c40b49d646e055e9b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 11 Apr 2016 09:27:41 +0100 Subject: [PATCH 0362/2403] Add missing zlib dep and change samtools to normal, not build dep --- .../b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index a786a5b208..9f5b2f295c 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -17,10 +17,14 @@ source_urls = ['https://github.com/genome/%(name)s/archive'] patches = ['%(name)s-%(version)s-cmake_install_prefix.patch'] builddependencies = [ - ('SAMtools', '1.3'), ('CMake', '3.4.1'), ] +dependencies = [ + ('SAMtools', '1.3'), + ('zlib', '1.2.8'), +] + prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&" separate_build_dir = True -- GitLab From a7b47e4ad40b160fb4989ad4cf48697e6006e266 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:34:28 +0200 Subject: [PATCH 0363/2403] foss 2016a version for sparsehash --- .../sparsehash/sparsehash-2.0.2-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb new file mode 100644 index 0000000000..062c5abe5e --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.2' + +homepage = 'https://code.google.com/p/sparsehash/' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sparsehash.googlecode.com/files/'] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file -- GitLab From 52b1c35a20d08cd618263ffe10d9108548360361 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:37:50 +0200 Subject: [PATCH 0364/2403] removed newline --- .../easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb index 062c5abe5e..d835154d86 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-foss-2016a.eb @@ -20,4 +20,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' -- GitLab From 8cf5d34294607fb7c056c4c581f26444a3152e68 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 10:45:57 +0200 Subject: [PATCH 0365/2403] foss 2016a version for ABySS --- .../a/ABySS/ABySS-1.9.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb new file mode 100644 index 0000000000..1aff3781e1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.9.0' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [('Boost', '1.60.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f7ac943a2ff6f9d2719bd0ca4d704cbf3af38622 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Apr 2016 11:52:51 +0200 Subject: [PATCH 0366/2403] add easyconfig pandas-0.18.0-intel-2016a-Python-2.7.11.eb, add easyconfig pandas-0.18.0-intel-2016a-Python-3.5.1.eb --- ...pandas-0.18.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ .../pandas-0.18.0-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..69e84f6fa3 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a3d2dbb5d1 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 446c86fc8446d9ceff2641644de5b40c79318f99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 12:33:47 +0200 Subject: [PATCH 0367/2403] Dependency of sparsehash --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 1aff3781e1..46ae6d041a 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -22,7 +22,10 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] -dependencies = [('Boost', '1.60.0')] +dependencies = [ + ('Boost', '1.60.0'), + (sparsehash, '2.0.2') +] sanity_check_paths = { 'files': ["bin/ABYSS", "bin/ABYSS-P"], -- GitLab From 807626f4d5d2ea884882a3fd8da582245e8726ee Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:44:56 +0200 Subject: [PATCH 0368/2403] add easyconfig Tcl-8.6.3-goolf-1.5.16.eb --- .../t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb new file mode 100644 index 0000000000..a8f55caa25 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 100f5c6abb616bfeb897c14a99b9023787f0ff6f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:52:11 +0200 Subject: [PATCH 0369/2403] Remove comment from HDF5-1.8.9-goolf-1.5.16.eb --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb index 755c2cc7f9..46dd3d15ad 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.1 on 2015-08-05_14-22-07 name = 'HDF5' version = '1.8.9' -- GitLab From c65cce06d6b0a92d173c96e87a6161f06a4b0a74 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 14:53:58 +0200 Subject: [PATCH 0370/2403] Comment out OpenSSL dependency in Python-2.7.9-goolf-1.5.16.eb --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index dee7cd4fdf..d726f06367 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -21,7 +21,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), - ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From 2d01f15bc0ff258e333b4110d1e60ba413e6dbb3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:03:51 +0200 Subject: [PATCH 0371/2403] Use https where possible in Python-2.7.9-goolf-1.5.16.eb --- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index d726f06367..70860e49fa 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -40,16 +40,16 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], }), ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 8acce97e99dd80a6fdad06c62cdc1f01b396b3fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:04:46 +0200 Subject: [PATCH 0372/2403] Correct preconfigopts in libreadline-6.3-goolf-1.5.16.eb --- .../easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb index 9a2a57c200..a11e7823ed 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.5.16.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 3752406eadac2b7d4b7f5b2f98a206b441b0d5de Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:14:10 +0200 Subject: [PATCH 0373/2403] Restrict parallel build in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index a11de24d4f..5af25d6b8e 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -23,6 +23,6 @@ configopts = '--with-jdk=$JAVA_HOME' preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' -buildopts = '-j 1' +parallel = 1 moduleclass = 'data' -- GitLab From 179a5fc322d8db28072e25ddf7c30851a389f14e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 11 Apr 2016 15:18:20 +0200 Subject: [PATCH 0374/2403] Wrap description to <120 characters in MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 5af25d6b8e..6a1d121ef8 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '7.0.67' versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://mdsplus.org/' -description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" +description = """MDSplus is a set of software tools for data acquisition and storage and a + methodology for management of complex scientific data.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From c9632d02a590714a1fa642a96e5229a88874c594 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Mon, 11 Apr 2016 15:24:37 +0200 Subject: [PATCH 0375/2403] add easyconfig numpy-1.11.0-intel-2016a-Python-2.7.11.eb --- .../numpy-1.11.0-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..cd8041b190 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' -- GitLab From fac75b00a9e17993cab3dce804a2aa753803ec2a Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Mon, 11 Apr 2016 15:55:23 +0200 Subject: [PATCH 0377/2403] Added patch --- .../n/numpy/numpy-1.11.0-sse42.patch | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch new file mode 100644 index 0000000000..75ffeaa0d5 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- ./numpy/distutils/intelccompiler.py.orig 2016-01-06 22:07:54.000000000 +0100 ++++ ./numpy/distutils/intelccompiler.py 2016-02-19 15:07:00.438235792 +0100 +@@ -54,7 +54,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + if platform.system() == 'Darwin': + shared_flag = '-Wl,-undefined,dynamic_lookup' +--- ./numpy/distutils/fcompiler/intel.py.orig 2016-01-07 03:16:25.000000000 +0100 ++++ ./numpy/distutils/fcompiler/intel.py 2016-02-19 15:07:16.424220745 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? -- GitLab From 472992ac0f7f131dcd519fa2fed53114f1a27e0f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:01:43 +0200 Subject: [PATCH 0378/2403] Beast latest version using foss-2016a --- .../b/Beast/Beast-2.4.0-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..68cf147acc --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Beast' +version = '2.4.0' + +homepage = 'http://beast2.org/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] + + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '2_1_2', '', ('foss', '2016a')), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a6397ef10bccd4aa65c1bc309b57c3a3cc40321d Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 11 Apr 2016 16:06:53 +0200 Subject: [PATCH 0379/2403] latest beagle-lib support foss2016a --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb new file mode 100644 index 0000000000..033afea4f8 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2_1_2' + +homepage = 'http://code.google.com/p/beagle-lib/' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%(version)s.tar.gz'] + +dependencies = [('Java', '1.7.0_15', '', True)] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 4712c5f28cbb0ec429d75facb3a9fd7cd2bc8e18 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 11 Apr 2016 17:25:00 +0200 Subject: [PATCH 0380/2403] Parallel version of IMa2 built with the foss/2016a toolchain. --- .../i/IMa2p/IMa2p-20151123-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb new file mode 100644 index 0000000000..d41195e663 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name ='IMa2p' +version = '20151123' +commit = '66e7ac7bc5e4c5bbadbd7de943465afeb4641770' + +homepage = 'https://github.com/arunsethuraman/ima2p' +description = """ +IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. http://dx.doi.org/10.1111/1755-0998.12437 +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/arunsethuraman/ima2p/archive/'] +sources = ['%s.zip' % commit] + +# If CXX is already set the compiler will not be changed to mpic++ by +# the configure. We therefore set it to mpic++. +preconfigopts = 'chmod +x configure && export CXX=mpic++ && ' +configopts = '--with-mpi=auto' + +sanity_check_paths = { + 'files': ['bin/IMa2p'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From edeed474f2fd36ab442256811a34bc917853649b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 11 Apr 2016 17:27:04 +0200 Subject: [PATCH 0381/2403] quickfix quotes for sparsehash dependency --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 46ae6d041a..442c127432 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -24,7 +24,7 @@ source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ ('Boost', '1.60.0'), - (sparsehash, '2.0.2') + ('sparsehash', '2.0.2') ] sanity_check_paths = { -- GitLab From e2ca621fcc6de9d3d7acd6a59c8f150370f1c588 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 14:48:56 -0400 Subject: [PATCH 0382/2403] using numpy 1.8.2 that support oldnumeric and makes compatible with Scientificpython --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ ...icPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index a597bd3eff..ef29eaf445 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', pyver), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for - ('numpy', '1.10.4', versionsuffix), + ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'Scientific'} -- GitLab From a947b9c9d89fc88a92ac4a55183a037922b70dad Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 15:04:46 -0400 Subject: [PATCH 0383/2403] add easyconfig numpy 1.8.2 for foss --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 ------------------- ...> numpy-1.8.2-foss-2016a-Python-2.7.11.eb} | 14 +++--- 2 files changed, 7 insertions(+), 51 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb rename easybuild/easyconfigs/n/numpy/{numpy-1.10.4-foss-2016a-Python-2.7.11.eb => numpy-1.8.2-foss-2016a-Python-2.7.11.eb} (82%) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 182905c4bb..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'Bundle' - -name = 'matplotlib' -version = '1.5.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -dependencies = [ - ('Python', '2.7.11'), - ('freetype', '2.6.2'), - ('libpng', '1.6.21'), -] - -exts_list = [ - ('Cycler', '0.9.0', { - 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'source_tmpl': 'cycler-%(version)s.tar.gz', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), -] - -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb similarity index 82% rename from easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index f2c859648a..e591de8fe1 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,6 +1,5 @@ name = 'numpy' -version = '1.10.4' -versionsuffix = '-Python-%(pyver)s' +version = '1.8.2' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -14,13 +13,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = [ - 'numpy-1.8.0-mkl.patch', - 'numpy-%(version)s-sse42.patch', -] +patches = ['numpy-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('Python', '2.7.11'), + (python, pyver), ] moduleclass = 'math' -- GitLab From af9773821329739f983ee9983353627e0b1d673c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 16:06:16 -0400 Subject: [PATCH 0384/2403] matplotlib 1.5.1 for foss 2016a --- ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..182905c4bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From d297900bdcad241d8e042b2c8136cd5f3044995b Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 11 Apr 2016 17:42:22 -0400 Subject: [PATCH 0385/2403] add easyconfig files for git 2.8.0 foss toolchain --- .../g/gettext/gettext-0.19.7-foss-2016a.eb | 23 +++++++++++++ .../easyconfigs/g/git/git-2.8.0-foss-2016a.eb | 33 +++++++++++++++++++ .../p/Perl/Perl-5.22.1-foss-2016a-bare.eb | 17 ++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb new file mode 100644 index 0000000000..168b2490e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb new file mode 100644 index 0000000000..37fb210f88 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.8.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.8.0' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.47.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.7'), + ('Perl', '5.22.1', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb new file mode 100644 index 0000000000..9234ed61fa --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From 48839f3594a14f4b645de4e827294b8ee99ae24b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 12 Apr 2016 16:57:34 +1200 Subject: [PATCH 0386/2403] New EasyConfig for Boost-1.60.0 with the foss-2015a toolchain --- .../b/Boost/Boost-1.60.0-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb new file mode 100644 index 0000000000..76d7cbc284 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From c35baf4c311b0abecf3fb9e6942386f6bca79b0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:35:06 +0200 Subject: [PATCH 0387/2403] correctly specify Perl location in git easyconfig --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 6a03e95dba..d8dcaa74d8 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From 3ab69db466b5c4491146598c3e23f17c9fc52191 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:03 +0200 Subject: [PATCH 0388/2403] add easyconfig MultiNest-3.10-intel-2016a.eb --- .../m/MultiNest/MultiNest-3.10-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb new file mode 100644 index 0000000000..78d3266bf6 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiNest/MultiNest-3.10-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MultiNest' +version = '3.10' + +homepage = 'https://ccpforge.cse.rl.ac.uk/gf/project/multinest/' +description = """MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space + which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# download via https://ccpforge.cse.rl.ac.uk/gf/project/multinest/frs (requires registration) +sources = ['MultiNest_v%(version)s_CMake.tar.gz'] +checksums = ['a4ed7c15f2fbbf7f859f565734fc5296'] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ackley', 'eggboxC', 'eggboxC++', 'gaussian', 'gauss_shell', 'himmelblau', + 'obj_detect', 'rosenbrock']] + + ['lib/lib%s' % x for x in ['multinest.a', 'multinest_mpi.a', 'multinest_mpi.%s' % SHLIB_EXT, + 'multinest.%s' % SHLIB_EXT]] + + ['include/multinest.h'], + 'dirs': ['modules'], +} + +moduleclass = 'tools' -- GitLab From 04e53f7a24ab360a3f3812526116aafc8a73a421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:39:58 +0200 Subject: [PATCH 0389/2403] fix typo --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index d8dcaa74d8..1da07f9d58 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -36,7 +36,7 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT}/bin/perl --enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" sanity_check_paths = { 'files': ['bin/git'], -- GitLab From fbb3f0cd75ab28fb77e3c558f35ab2a8c6117da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 09:42:31 +0200 Subject: [PATCH 0390/2403] add easyconfig CMake-3.5.1-intel-2016a.eb --- .../c/CMake/CMake-3.5.1-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb new file mode 100644 index 0000000000..a70441375c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d2dbcc47e9b38f23d53272986bfbc28aa15faaaf Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:32:03 +0200 Subject: [PATCH 0391/2403] fix beagle-lib dependency --- easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb index 68cf147acc..484da63909 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -21,12 +21,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.Linux.tgz'] - dependencies = [ # this is not mandatory but beagle-lib is recommended by developers # beagle-lib will also load the required java dependency # if you remove this you should add the java dependency - ('beagle-lib', '2_1_2', '', ('foss', '2016a')), + ('beagle-lib', '2.1.2'), ] sanity_check_paths = { -- GitLab From 2b7c6d3f7ccd97633b3f77e36d3083ecc8135c8f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 11:34:32 +0200 Subject: [PATCH 0392/2403] fix java version, naming, builddependencies --- .../beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb new file mode 100644 index 0000000000..29785ed5e6 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '2.1.2' +homepage= 'https://github.com/beagle-dev/beagle-lib' +description = """ +beagle-lib is a high-performance library that can perform the core +calculations at the heart of most Bayesian and Maximum Likelihood +phylogenetics packages. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] + +dependencies = [('Java', '1.8.0_74', '', True)] + +builddependencies = [('Autotools', '20150215')] + +# parallel build does not work (to test) +parallel = 1 + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 18e01e189a43b9ad3c3f6c356919cb8808dd7f39 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Apr 2016 13:25:43 +0200 Subject: [PATCH 0393/2403] removed bad beagle-lib --- .../beagle-lib/beagle-lib-2_1_2-foss-2016a.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb deleted file mode 100644 index 033afea4f8..0000000000 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2_1_2-foss-2016a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'beagle-lib' -version = '2_1_2' - -homepage = 'http://code.google.com/p/beagle-lib/' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz -source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] -sources = ['beagle_release_%(version)s.tar.gz'] - -dependencies = [('Java', '1.7.0_15', '', True)] - -# parallel build does not work (to test) -parallel = 1 - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile - for includefile in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], - 'dirs': [] -} - -moduleclass = 'numlib' -- GitLab From 4a944ea2fd093c34ea0941a39499c694fd26d6b0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 14:32:26 +0200 Subject: [PATCH 0394/2403] dependency for SQLite --- easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index 442c127432..aa09a6e789 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -23,8 +23,9 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [ - ('Boost', '1.60.0'), - ('sparsehash', '2.0.2') + ('Boost', '1.60.0'), + ('sparsehash', '2.0.2'), + ('SQLite', '3.9.2'), ] sanity_check_paths = { -- GitLab From 7724b2dfaa1a7cfb474d0c1c7b188dd796ce53b3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 15:42:21 +0200 Subject: [PATCH 0395/2403] ANTLR with foss 2016a --- .../ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a69233b272 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = "2.7.7" + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +pythonversion = '2.7.11' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('Java', '1.8.0_74', '', True), + ('Python', pythonversion), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' -- GitLab From 2b1307343774ae1202878dfafa731a4a6d2f09d0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:46:02 +0200 Subject: [PATCH 0396/2403] BayesAss with foss 2016a --- .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb new file mode 100644 index 0000000000..3e78699b7f --- /dev/null +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BayesAss' +version = '3.0.3' + +homepage = 'http://www.rannala.org/?page_id=245' description = """ +BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +sources = ['BA3-%(version)s.tar.gz'] +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % +version] +dependencies = [ + ('GSL','1.16') +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'dirs' : ['bin','include'] +} + +moduleclass = 'bio' -- GitLab From d2f300a14948c1357a37e95079bbccaeab5a2b13 Mon Sep 17 00:00:00 2001 From: perettig Date: Tue, 12 Apr 2016 16:50:54 +0200 Subject: [PATCH 0397/2403] renamed DCA++ eb file --- .../DCA++-CMake-CrayGNU-2015.11-cuda.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/d/{DCA/DCA++-CMake-CrayGNU-2015.11.eb => DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb} (100%) diff --git a/easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb b/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb similarity index 100% rename from easybuild/easyconfigs/d/DCA/DCA++-CMake-CrayGNU-2015.11.eb rename to easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb -- GitLab From 4a1fe16ac37a29bdf91da0c140fc6b92f3e7809d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 16:54:33 +0200 Subject: [PATCH 0398/2403] newline added --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 3e78699b7f..9f74a15dd0 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -3,7 +3,8 @@ easyblock = 'ConfigureMake' name = 'BayesAss' version = '3.0.3' -homepage = 'http://www.rannala.org/?page_id=245' description = """ +homepage = 'http://www.rannala.org/?page_id=245' +description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -- GitLab From 441d862ecefdf2adc6222a07a7b2129f618ec502 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:09:00 +0200 Subject: [PATCH 0399/2403] HTSlib for foss 2016a --- .../h/HTSlib/HTSlib-1.3-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb new file mode 100644 index 0000000000..7f85666c7d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.3' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From 6e446908e5bb57328bccdb45bc08d8e751ec8fa9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:11:17 +0200 Subject: [PATCH 0400/2403] removed newline --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb index 7f85666c7d..93d7d3c6df 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From bd6af2e81b9f53060da3ebb1a51fc7abdd4f69ae Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:13:57 +0200 Subject: [PATCH 0401/2403] BCFtools for foss 2016a --- .../b/BCFtools/BCFtools-1.3-foss-2016a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb new file mode 100644 index 0000000000..fe8eabe029 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.3' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.3'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), +] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' -- GitLab From 0330bcc156ccb9096c94cdee4b1c7c9c479577db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Apr 2016 17:23:53 +0200 Subject: [PATCH 0402/2403] quickfix version number --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 9f74a15dd0..b10287dfdd 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' name = 'BayesAss' -version = '3.0.3' +version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % version] @@ -19,7 +19,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["BA3"]], + 'files': [bin/BA3], 'dirs' : ['bin','include'] } -- GitLab From da26578e66c29d9448e012483a1af10a2166b073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:26:13 +0200 Subject: [PATCH 0403/2403] add missing 'easyblock' spec in libunwind easyconfig file --- .../l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index 5a47aa7676..cdac53c708 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -6,6 +6,8 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## +easyblock = 'ConfigureMake' + name = 'libunwind' version = '1.1' @@ -18,13 +20,9 @@ description = """The primary goal of this project is to define a portable and ef toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], 'dirs': [], -- GitLab From b824736fb1f0ecb20854c4d1f6cb09a463413246 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:29:47 +0200 Subject: [PATCH 0404/2403] add missing 'easyblock' line in Extrae easyconfig + comments in Extrae patch file --- .../Extra-2.4.1_configure-no-shared-binutils.patch | 2 ++ .../e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 10 ++++++---- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch index 8b712760c3..c2fc719e06 100644 --- a/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch +++ b/easybuild/easyconfigs/e/Extrae/Extra-2.4.1_configure-no-shared-binutils.patch @@ -1,3 +1,5 @@ +fix configure tests for libbfd.a +author: Bernd Mohr (Juelich Supercomputing Centre, Germany) --- configure.orig 2013-11-11 16:38:11.872367495 +0100 +++ configure 2013-11-11 16:38:32.872767289 +0100 @@ -27477,9 +27477,9 @@ diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index d8500be6ba..a73fcf181f 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -6,6 +6,8 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## +easyblock = 'ConfigureMake' + name = "Extrae" version = "2.4.1" @@ -24,7 +26,7 @@ toolchainopts = {"usempi": True} # Requires input of email address for download sources = [SOURCELOWER_TAR_BZ2] -patches = ['Extra-2.4.1_configure-no-shared-binutils.patch'] +patches = ['Extra-%(version)s_configure-no-shared-binutils.patch'] # compiler toolchain depencies dependencies = [ @@ -35,6 +37,9 @@ dependencies = [ ('PAPI', '5.2.0'), ] +# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC +preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' + configopts = ' --with-mpi=${EBROOTOPENMPI}' configopts += ' --with-papi=${EBROOTPAPI} --enable-sampling' configopts += ' --enable-xml --enable-merge-in-trace' @@ -42,11 +47,8 @@ configopts += ' --with-unwind=${EBROOTLIBUNWIND}' configopts += ' --without-dwarf --without-dyninst' configopts += ' --with-boost=${EBROOTBOOST}' configopts += ' --with-binutils=${EBROOTBINUTILS}' -# make sure libbfd.a/libiberty.a provided by binutils is used rather than the ones provided by GCC -preconfigopts = 'export LDFLAGS="-L${EBROOTBINUTILS}/lib -L${EBROOTBINUTILS}/lib64 $LDFLAGS" && ' # --- BM EXTENSIONS --- -# # Extrae also supports CUDA measurements - not yet tested # configopts += ' --with-cuda=${EBROOTCUDA} --with-cupti=${EBROOTCUDA}/extras/CUPTI' -- GitLab From 63ddc7705a012695122cc6a7b58db2d13618d9d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:30:54 +0200 Subject: [PATCH 0405/2403] minor change to osdeps in Boost easyconfig --- .../easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb index 3e994ae064..621e1934a4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -17,6 +17,6 @@ configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -osdependencies = ['zlib-devel'] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' -- GitLab From 0387f648baf38ac56a0ac5b9f41ff9851ba879e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Apr 2016 17:54:38 +0200 Subject: [PATCH 0406/2403] fix name of Boost serial easyconfig --- ....53.0-serial-GCC-4.7.3.eb => Boost-1.53.0-GCC-4.7.3-serial.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/Boost/{Boost-1.53.0-serial-GCC-4.7.3.eb => Boost-1.53.0-GCC-4.7.3-serial.eb} (100%) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.53.0-serial-GCC-4.7.3.eb rename to easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb -- GitLab From e4b84a2bc7e5e6f95e21523fb6b05320e33780a9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:29:39 -0500 Subject: [PATCH 0407/2403] Changing the version (Date Format) and also adding instructions to rename the downloaded file to lx-%(version)s.zip --- easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb index 69196eb784..9830a06815 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb @@ -5,7 +5,7 @@ easyblock = "PackedBinary" name = 'MRIcron' -version = '06_22_15' +version = '20150601' homepage = 'http://www.mccauslandcenter.sc.edu/mricro/mricron/' description = """ MRIcron allows viewing of medical images. It @@ -17,8 +17,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ -# and place it in a folder where Easybuild can see it. -sources = ['lx.zip'] +# and place it in a folder where Easybuild can see it. +# Also rename the zip file to lx-20150601.zip +sources = ['lx-%(version)s.zip'] checksums = ['a2d8b1c053384220953f6b670d0fd4df'] -- GitLab From d25771501a9f87623f013f7f34c643b824846f50 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 12 Apr 2016 15:51:36 -0500 Subject: [PATCH 0408/2403] Renaming the Easyconfig from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb -> easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb --- .../m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MRIcron/{MRIcron-06_22_15.eb => MRIcron-20150601.eb} (100%) diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb similarity index 100% rename from easybuild/easyconfigs/m/MRIcron/MRIcron-06_22_15.eb rename to easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb -- GitLab From 428e635f7c6c76b6e89bba45dc64e263930df681 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 12 Apr 2016 23:01:13 +0200 Subject: [PATCH 0409/2403] Add missing zlib dependency to MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 6a1d121ef8..b1dbee0965 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -17,7 +17,8 @@ dependencies = [ ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), - ('libxml2', '2.9.3', '-Python-%(pyver)s') + ('libxml2', '2.9.3', '-Python-%(pyver)s'), + ('zlib', '1.2.8') ] configopts = '--with-jdk=$JAVA_HOME' -- GitLab From 2a277f236dbba0ad4e31f680f65d5ac4f5d4da27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 07:35:25 +0200 Subject: [PATCH 0410/2403] fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 1 + .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 3 +++ 3 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb index 2966a85fa7..a289e5fb02 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a.eb @@ -28,9 +28,13 @@ dependencies = [ ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 2b4eff3bde..2d93058e5e 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), + ('libpthread-stubs', '0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index eee347a314..1e63340752 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -14,6 +14,9 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28') ] dependencies = [ -- GitLab From b9067f93645bb3e7ac817334393b612f4d21ad47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 10:50:26 +0200 Subject: [PATCH 0411/2403] fix (pyver)s --- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index a69233b272..ddbfe7c092 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'ANTLR' version = "2.7.7" +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.antlr2.org/' description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) @@ -16,12 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] -pythonversion = '2.7.11' -versionsuffix = "-Python-%s" % pythonversion - dependencies = [ ('Java', '1.8.0_74', '', True), - ('Python', pythonversion), + ('Python', '2.7.11'), ] configopts = '--disable-examples --disable-csharp ' -- GitLab From 46471130a735bf0c4bcc673d57e4f92dc0128e01 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 13 Apr 2016 10:19:44 +0100 Subject: [PATCH 0412/2403] Update rtracklayer to 1.30.4 --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 2 +- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 78a36e128c..60ddc2ec31 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -80,7 +80,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 42093e636a..75d2568589 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -79,7 +79,7 @@ exts_list = [ ('DEGseq', '1.24.0', bioconductor_options), ('hgu133plus2.db', '3.2.2', bioconductor_options), ('illuminaio', '0.12.0', bioconductor_options), - ('rtracklayer', '1.30.3', bioconductor_options), + ('rtracklayer', '1.30.4', bioconductor_options), ('biomaRt', '2.26.1', bioconductor_options), ('GenomicFeatures', '1.22.13', bioconductor_options), ('bumphunter', '1.10.0', bioconductor_options), -- GitLab From b38448a86b6ed9d38ab6d5653d2582a50ddbae0d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:21 +0200 Subject: [PATCH 0413/2403] quickfixes, but still needs GSL-2.1 dependency --- .../easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index b10287dfdd..ba5608e32b 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -10,8 +10,9 @@ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes toolchain = {'name': 'foss','version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] -source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%s/src/' % -version] + +source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] + dependencies = [ ('GSL','1.16') ] @@ -20,7 +21,7 @@ runtest = 'check' sanity_check_paths = { 'files': [bin/BA3], - 'dirs' : ['bin','include'] + 'dirs' : ['bin', 'include'] } moduleclass = 'bio' -- GitLab From 49bf25ee263585f62beec59942007be8f3dbce47 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:39:49 +0200 Subject: [PATCH 0414/2403] GSL-2.1 dependency --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index ba5608e32b..97b9dbe142 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -14,7 +14,7 @@ sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] dependencies = [ - ('GSL','1.16') + ('GSL','2.1') ] runtest = 'check' -- GitLab From 2de7a18c82c6442ebb2bc246fbb2964a4c4ce511 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:42:36 +0200 Subject: [PATCH 0415/2403] GSL for foss 2016a --- .../easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..f4a28c0d8f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = "2.1" + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'version': '2016a', 'name': 'foss'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From db2effc74e8f575a3632e68206455bab132a3fcd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 11:49:49 +0200 Subject: [PATCH 0416/2403] missing quotes --- easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 97b9dbe142..0dc4a540af 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ runtest = 'check' sanity_check_paths = { - 'files': [bin/BA3], + 'files': ['bin/BA3'], 'dirs' : ['bin', 'include'] } -- GitLab From 84b85cd3604256e9af2be975196276df1bf66c5c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 12:04:52 +0200 Subject: [PATCH 0417/2403] GSL dependency from 1.16 -> 2.1 --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index fe8eabe029..3e9dc817b1 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -18,7 +18,7 @@ patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] dependencies = [ ('HTSlib', '1.3'), ('zlib', '1.2.8'), - ('GSL', '1.16'), + ('GSL', '2.1'), ] parallel = 1 -- GitLab From 2f99209ef3e70c349dc29e7e5d417d1e1ea95000 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 12:33:26 +0200 Subject: [PATCH 0418/2403] Update plumed to intel/2016a --- .../b/byacc/byacc-20160324-intel-2016a.eb | 22 ++++++++++ .../libmatheval-1.1.11-intel-2016a.eb | 33 +++++++++++++++ .../p/PLUMED/PLUMED-2.2.1-intel-2016a.eb | 42 +++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb new file mode 100644 index 0000000000..a80f721d5e --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160324' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['bde0463c6c03f059b1e6e9c5579cbe49'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb new file mode 100644 index 0000000000..69ffa90aab --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160324'), + ('guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb new file mode 100644 index 0000000000..eff628072a --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 655557655eddce27838ed78a0fcdd2e01f947901 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 12:40:04 +0200 Subject: [PATCH 0419/2403] Update CP2K to use newest PLUMED --- easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb index 9d0e4f481b..be60b5e88f 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -21,6 +21,7 @@ patches = [ dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.2'), + ('PLUMED', '2.2.1'), ] builddependencies = [ @@ -28,6 +29,8 @@ builddependencies = [ ('Bison', '3.0.4'), ] +plumed = True + # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed parallel = 1 -- GitLab From f8941af3095fdf106df4e80d4a7e56ee8d96fde2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:30:15 +0200 Subject: [PATCH 0420/2403] dos newlines to unix --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..c3ca739024 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.6.924' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB_File', '1.835', versionsuffix), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From 2d8bab7056a653924682ff0c75bed5b2b9eb77f9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:57:19 +0200 Subject: [PATCH 0421/2403] DB_File for foss 2016a --- .../DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..b280622820 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.835' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('DB', '4.8.30'), +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From e65dfd7e88dc147706ce2f11c886b93549b6862e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 16:59:20 +0200 Subject: [PATCH 0422/2403] DB with foss 2016a --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb new file mode 100644 index 0000000000..0db26d6d7e --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '4.8.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' -- GitLab From 9c45c9617c8e9beeb9bf697457d644b33c664b3d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 17:02:48 +0200 Subject: [PATCH 0423/2403] biopython with foss 2016a --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From b8685d0c7ed5148f294eb805515dae58af8714b9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 17:41:43 +0200 Subject: [PATCH 0424/2403] Add libxsmm --- .../l/libxsmm/libxsmm-1.4-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb new file mode 100644 index 0000000000..e6719ce261 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' -- GitLab From 53fa6574b2414a86eb27c279bfe5e4032c76703f Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 13 Apr 2016 17:49:24 +0200 Subject: [PATCH 0425/2403] removed unused dependency (cmake) --- easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index f6daad29dd..c95dfaeaaf 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -16,8 +16,7 @@ source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] skipsteps = ['configure'] -builddependencies = [ ('CMake', '3.5.0'), - ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] +builddependencies = [ ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] sanity_check_paths={ 'files': ['lib/libmagma.so', 'lib/libmagma.a'], -- GitLab From f41070db77f5eec9d76f3d28e9ff2fbbab6cc607 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 13 Apr 2016 11:56:18 -0400 Subject: [PATCH 0426/2403] PGI: add easyconfig for version 16.3. --- .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..def0637f0b --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['618cb7ddbc57d4e4ed1f21a0ab25f427'] + +gccver = '4.9.3' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") + +moduleclass = 'compiler' -- GitLab From d4aba5b03e694f4e89d23260d4aaf6625dcb2c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Apr 2016 18:53:09 +0200 Subject: [PATCH 0427/2403] fix bitstring 3.1.3 download URL --- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 6 ++++-- .../easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 6 ++++-- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 6 ++++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 6 ++++-- 6 files changed, 24 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index b360b95e8c..51bd3f9ff0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 2556554c13..80212964f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -123,8 +123,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 9c41844d2f..a99feb7078 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 3976e80bf2..bce00fd447 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 62884700e2..0965b7d1e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -128,8 +128,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 1ecb34bdf1..1468388148 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -126,8 +126,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], }), ('virtualenv', '14.0.5', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], -- GitLab From ea5d4a30da2d8caaede51155c211321b3817f9c7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Apr 2016 21:06:48 +0200 Subject: [PATCH 0428/2403] buildopts added --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 3e9dc817b1..6d469bdd3b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -25,6 +25,7 @@ parallel = 1 skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' installopts = ' prefix=%(installdir)s' postinstallcmds = [ -- GitLab From 3aed66b4731165b057fa9396425c15ab63f5971a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 14 Apr 2016 11:07:18 +0800 Subject: [PATCH 0429/2403] initial support for ABINIT-7.10.5 with intel-2016.02-GCC-4.9 toolchain --- .../ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d59f27574e --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,24 @@ +# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 +# --try-toolchain=intel,2016.02-GCC-4.9, worked but it seems to at least lack mpi support +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' + -- GitLab From 81be1a45da8cdbe335fe23b0a0a6cf396c8512d2 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:10 -0700 Subject: [PATCH 0430/2403] OptiX 3.8.0: fix easyconfig issues --- .../o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index db096d2117..a4d1d070ca 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -3,6 +3,7 @@ # Authors:: Stephane Thiell ## easyblock = 'Binary' + name = 'OptiX' version = '3.8.0' @@ -13,21 +14,26 @@ description = """OptiX is NVIDIA SDK for easy ray tracing performance. toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} -#source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] - +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run + '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.so", "lib64/liboptixu.so"], + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -modextravars = { 'OPTIX_HOME': '%(installdir)s' } +modextravars = {'OPTIX_HOME': '%(installdir)s'} moduleclass = 'vis' -- GitLab From 83165bc9263c9bd20569d013fda4c8b7c68a3711 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:29:41 -0700 Subject: [PATCH 0431/2403] add Nvidia OptiX 3.9.0 easyconfig --- .../o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..c8c1772071 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +easyblock = 'Binary' + +name = 'OptiX' +version = '3.9.0' + +homepage = 'https://developer.nvidia.com/optix' +description = """OptiX is NVIDIA SDK for easy ray tracing performance. + It provides a simple framework for accessing the GPU’s massive ray tracing + power using state-of-the-art GPU algorithms.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +# Registration required. Download links: +# https://developer.nvidia.com/designworks/optix/download +# https://developer.nvidia.com/designworks/optix/downloads/legacy +sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.sh'] + +checksums = [ + '13b1953af766b82e0a4aaa28766a05a1', # NVIDIA-OptiX-SDK-3.9.0-linux64.sh +] + +install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ["include/optix.h", + "include/optix_cuda.h", + "lib64/liboptix.%s" % SHLIB_EXT, + "lib64/liboptixu.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextravars = {'OPTIX_HOME': '%(installdir)s'} + +moduleclass = 'vis' -- GitLab From 0a8d27bcbf785078454859c00a483c64a99cd40b Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 22:54:42 -0700 Subject: [PATCH 0432/2403] add easyconfig for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb new file mode 100644 index 0000000000..e6b47b55c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '7.0.28' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From e1f57b8fb0e64c025494208f50636c69c0cd6797 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 14 Apr 2016 07:25:03 +0100 Subject: [PATCH 0433/2403] Updates for limma, edgeR, Gviz, Rsubread --- .../R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb | 8 ++++---- .../R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 60ddc2ec31..13ad83c774 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -62,7 +62,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -70,7 +70,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -126,13 +126,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 75d2568589..64a35be205 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -61,7 +61,7 @@ exts_list = [ ('preprocessCore', '1.32.0', bioconductor_options), ('affy', '1.48.0', bioconductor_options), ('GO.db', '3.2.2', bioconductor_options), - ('limma', '3.26.8', bioconductor_options), + ('limma', '3.26.9', bioconductor_options), ('RBGL', '1.46.0', bioconductor_options), ('org.Hs.eg.db', '3.2.3', bioconductor_options), ('AnnotationForge', '1.12.2', bioconductor_options), @@ -69,7 +69,7 @@ exts_list = [ ('annaffy', '1.42.0', bioconductor_options), ('gcrma', '2.42.0', bioconductor_options), ('oligoClasses', '1.32.0', bioconductor_options), - ('edgeR', '3.12.0', bioconductor_options), + ('edgeR', '3.12.1', bioconductor_options), ('PFAM.db', '3.2.2', bioconductor_options), ('perm', '1.0-0.0', ext_options), ('baySeq', '2.4.1', bioconductor_options), @@ -125,13 +125,13 @@ exts_list = [ ('Mfuzz', '2.30.0', bioconductor_options), ('maSigPro', '1.42.0', bioconductor_options), ('SPIA', '2.22.0', bioconductor_options), - ('Gviz', '1.14.4', bioconductor_options), + ('Gviz', '1.14.7', bioconductor_options), ('cummeRbund', '2.12.1', bioconductor_options), ('GenomicFiles', '1.6.2', bioconductor_options), ('derfinderHelper', '1.4.1', bioconductor_options), ('derfinder', '1.4.4', bioconductor_options), ('polyester', '1.6.0', bioconductor_options), - ('Rsubread', '1.20.3', bioconductor_options), + ('Rsubread', '1.20.5', bioconductor_options), ('pcaMethods', '1.60.0', bioconductor_options), ('marray', '1.48.0', bioconductor_options), ('CGHbase', '1.30.0', bioconductor_options), -- GitLab From 52f5d1c9486f961db52a9ec2ff4373b760e0d539 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:34:11 -0700 Subject: [PATCH 0434/2403] add easyconfig for cuDNN 4.0 and 5.0 --- easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb | 32 ++++++++++++++++++++++ easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb | 32 ++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb new file mode 100644 index 0000000000..5bcd0e1aa3 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '4.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.0-linux-x64-v%(version)s-prod.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '845ead4b37f1a2a243d7d1b4d42d1d8b', # cudnn-7.0-linux-x64-v4.0-prod.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb new file mode 100644 index 0000000000..fcf816c8fb --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.0' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] + +dependencies = [('CUDA', '7.5.18')] + +checksums = [ + '0febee3f11276218668857191514b7e0', # cudnn-7.5-linux-x64-v5.0-rc.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 0de0c65aa8aee81d2dbb094481227bf4976ca9dd Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:52:00 -0700 Subject: [PATCH 0435/2403] OptiX: fix a few issues --- easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb | 5 +---- easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb | 4 +--- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index a4d1d070ca..69dec5c347 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -21,15 +21,12 @@ sources = ['NVIDIA-OptiX-SDK-%(version)s-linux64.run'] checksums = [ 'ecf63cf32b87defa36d3cd283d085314', # NVIDIA-OptiX-SDK-3.8.0-linux64.run - '73eb689d6247e3d406cf3a38e80ec473', # NVIDIA-OptiX-SDK-3.7.0-linux64.run ] install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb index c8c1772071..7960265e87 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -26,9 +26,7 @@ checksums = [ install_cmd = "./" + sources[0] + " --skip-license --prefix=%(installdir)s" sanity_check_paths = { - 'files': ["include/optix.h", - "include/optix_cuda.h", - "lib64/liboptix.%s" % SHLIB_EXT, + 'files': ["include/optix.h", "include/optix_cuda.h", "lib64/liboptix.%s" % SHLIB_EXT, "lib64/liboptixu.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 278865b55584db402d5cbe24ffd599c6b90a0d0e Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Wed, 13 Apr 2016 23:59:34 -0700 Subject: [PATCH 0436/2403] remove CUDA_HOME modext as it is already handled by easyblock --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index e6b47b55c2..87e535776e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -13,6 +13,4 @@ source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_majo sources = ['%(namelower)s_%(version)s_linux.run'] -modextravars = {'CUDA_HOME': '%(installdir)s'} - moduleclass = 'system' -- GitLab From 4a4426f75304e17e6e10c50200e4527aa4f8fd32 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 09:37:21 +0200 Subject: [PATCH 0437/2403] Add ALPS --- .../ALPS-2.2b4-intel-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..27a5876ff2 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'ALPS' +version = '2.2b4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.example.com' +description = """ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort +aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ +libraries for simplifying the development of such code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://alps.comp-phys.org/static/software/releases'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('HDF5', '1.8.16'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'phys' -- GitLab From c972ef56ffd0e56fa124971f5ef54666cf5b5bae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:16:24 +0200 Subject: [PATCH 0438/2403] add easyconfig Perl-5.20.3-intel-2015a.eb --- .../p/Perl/Perl-5.20.3-intel-2015a.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb new file mode 100644 index 0000000000..e4d3b47d6f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015a.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD/'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' -- GitLab From 5baa6d14a4f0a16626d4317e433b63f618984f40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 10:22:07 +0200 Subject: [PATCH 0439/2403] fix Perl dependency in worker, it required non-standard Perl modules --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index e3023d8f2c..cdf0174497 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('Perl', '5.20.1', '-bare') + ('Perl', '5.20.3') ] # adjust worker configuration file -- GitLab From c8354ece8ecb261c40e561951d32c1d0c002684f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:10:24 +0200 Subject: [PATCH 0440/2403] add easyconfig dask-0.8.2-intel-2016a-Python-2.7.11.eb --- .../dask-0.8.2-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..10a9f3bf36 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 15df4db6a6f422c44e7f33a2f203776aca51fd47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:16:45 +0200 Subject: [PATCH 0441/2403] add easyconfig dask-0.8.2-intel-2016a-Python-3.5.1.eb --- .../dask-0.8.2-intel-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..7dcf741ab4 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.8.2-intel-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From a34e72227fe18a01ef50128de64d8b9dd7aab7ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 13:41:02 +0200 Subject: [PATCH 0442/2403] add easyconfig worker-1.6.4-intel-2016a.eb --- .../w/worker/worker-1.6.4-intel-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb new file mode 100644 index 0000000000..3c373e597a --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.4' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.1') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) +] + +moduleclass = 'tools' -- GitLab From 942d3126ede0f528f12f643439eab5b7d96d7043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Apr 2016 14:35:01 +0200 Subject: [PATCH 0443/2403] add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 782d02fe62..c11711336f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 5dcd8c848b..f0600eefc0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), ('GMP', '6.1.0'), + ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From c9dd68acf5e40c1f285cc47073077135a7c24887 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 14 Apr 2016 08:38:54 -0400 Subject: [PATCH 0444/2403] PGI: adjust license file (suggested by @boegel) and add numactl-GCCcore dependency. --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 25 +++++++++++++++++++ .../p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb | 4 +-- 2 files changed, 27 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..e54c32859f --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb index def0637f0b..1b4b9a4866 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -16,10 +16,10 @@ versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), ] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' -- GitLab From e913f23e064c6018bcd09084aebc10d61b54e7ea Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 14:51:53 +0200 Subject: [PATCH 0445/2403] Almost there for ALPS --- ...1.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/ALPS/{ALPS-2.2b4-intel-2016a-Python-2.7.11.eb => ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb} (73%) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb similarity index 73% rename from easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index 27a5876ff2..cf98c0aae4 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ALPS' -version = '2.2b4' +version = '2.2.b4' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.example.com' @@ -17,12 +17,20 @@ source_urls = ['http://alps.comp-phys.org/static/software/releases'] builddependencies = [('CMake', '3.4.3')] dependencies = [ + ('zlib', '1.2.8'), ('Python', '2.7.11'), - ('Boost', '1.60.0', versionsuffix), + ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] +configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' +configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' + +separate_build_dir = True + +maxparallel = 1 + sanity_check_paths = { 'files': [], 'dirs': ["."] -- GitLab From 34d060379900bd4976c8d08fdcaba2b81ae33041 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 14:53:28 +0200 Subject: [PATCH 0446/2403] Add libxsmm to CP2k --- easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb index be60b5e88f..a4b8c3995d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.2'), ('PLUMED', '2.2.1'), + ('libxsmm', '1.4'), ] builddependencies = [ -- GitLab From 8e87dab94667a21f1e994e7548b7bfc681751c91 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:12:02 +0200 Subject: [PATCH 0447/2403] Add Boost 1.58 for intel/2016a --- .../Boost-1.58.0-intel-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f392ae7ad4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From e9dedd35e4fdb96140766e12e25dc1be849b8708 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:35:32 +0200 Subject: [PATCH 0448/2403] Add MariaDB 10.1.13 --- .../j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 23 +++++++++++++++ .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 29 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb new file mode 100644 index 0000000000..76daf74962 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.1.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.canonware.com/download/jemalloc/'] +sources = [SOURCE_TAR_BZ2] + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb new file mode 100644 index 0000000000..e373db06bd --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.13' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses', '6.0'), + ('jemalloc', '4.1.0'), +] + +builddependencies = [('CMake', '3.4.3')] + +#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From f1eefdcb7cbdca66815ced46a8c94986afd8e219 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:37:25 +0200 Subject: [PATCH 0449/2403] jemalloc: use github --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 76daf74962..840d6b9d2e 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -9,8 +9,8 @@ description = """jemalloc is a general purpose malloc(3) implementation that emp toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.canonware.com/download/jemalloc/'] -sources = [SOURCE_TAR_BZ2] +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 9b6344d8e154a27ab11b607c9fe36330c4c4d291 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:44:15 +0200 Subject: [PATCH 0450/2403] Use autogen for jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 840d6b9d2e..26a2f81a65 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/jemalloc/jemalloc/archive'] sources = ['%(version)s.tar.gz'] +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], -- GitLab From 57391a12530ca3fde36656478ed248ed9ecd0b3f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:49:35 +0200 Subject: [PATCH 0451/2403] Fix jemalloc build --- easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 26a2f81a65..59c52ac8e4 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -15,6 +15,7 @@ sources = ['%(version)s.tar.gz'] builddependencies = [('Autotools', '20150215')] preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, -- GitLab From 87d301508772d255d769f48a01cc79b066c30236 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 15:53:00 +0200 Subject: [PATCH 0452/2403] Fix sanity check of jemalloc --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index 59c52ac8e4..e13485c431 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -18,11 +18,11 @@ preconfigopts = "./autogen.sh && " prebuildopts = "make dist && " sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} moduleclass = 'lib' -- GitLab From 8269f5aec87a38fc6fbe0f645211ffda2364a038 Mon Sep 17 00:00:00 2001 From: Giovanni Date: Thu, 14 Apr 2016 16:07:03 +0200 Subject: [PATCH 0453/2403] implemented suggestion from Urs: added a cpu only configurations and a proper description --- .../DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb | 24 +++++++++++++++++++ .../DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb | 4 ++-- .../m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 1 - 3 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb b/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb new file mode 100644 index 0000000000..fa74423de4 --- /dev/null +++ b/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cpu.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'DCA++' +version = '1.0' +versionsuffix = '-cpu' + +#consider building everything with eb: +#preinstallopts: change build_directory +#disable clean build directory + +homepage = 'http://www.itp.phys.ethz.ch/research/comp/computation.html' +description = """The DCA++ software project is a C++ implementation of the dynamical cluster approximation (DCA) and its DCA+ extension. It aims to solve lattice models of strongly correlated electron systems. This module bundles all the dependencies and does not make use of the GPU.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +dependencies = [ + ('CMake', '3.5.0'), + ('spglib', '1.7.3'), + ('NFFT', '3.3.0'), + ('gtest', '1.7.0'), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb b/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb index 7d57829763..43f2e42796 100644 --- a/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb +++ b/easybuild/easyconfigs/d/DCA++/DCA++-CMake-CrayGNU-2015.11-cuda.eb @@ -8,8 +8,8 @@ versionsuffix = '-cuda' #preinstallopts: change build_directory #disable clean build directory -homepage = 'http://www.itp.phys.ethz.ch/people/schulthess' -description = """This modules bundles all the dependencies for DCA++, the best DCA ever""" +homepage = 'http://www.itp.phys.ethz.ch/research/comp/computation.html' +description = """The DCA++ software project is a C++ implementation of the dynamical cluster approximation (DCA) and its DCA+ extension. It aims to solve lattice models of strongly correlated electron systems. This module bundles all the dependencies.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index c95dfaeaaf..6d65acbcdf 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -26,4 +26,3 @@ sanity_check_paths={ patches = [('magma-2.0.0.patch')] moduleclass = 'math' - -- GitLab From 494835b0f6103687cafe2ccb67e54767058a8651 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:20:47 +0200 Subject: [PATCH 0454/2403] Add options to MariaDB --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index e373db06bd..dc6e52c840 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -15,11 +15,13 @@ dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), + ('PCRE', '8.38'), + ('XZ', '5.2.2'), ] builddependencies = [('CMake', '3.4.3')] -#configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], -- GitLab From b1e18a3183cb74b9ad3de414a1610cadfb7a7f98 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 16:54:14 +0200 Subject: [PATCH 0455/2403] Even more deps for MariaDB --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index dc6e52c840..68f736cb1a 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), + ('Boost', '1.60.0'), + ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -- GitLab From e8ddbaeb437dc2dd0d5f91184e5872522e2a5aee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 17:37:34 +0200 Subject: [PATCH 0456/2403] Add PostgreSQL 9.5.2 --- .../PostgreSQL-9.5.2-intel-2016a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb new file mode 100644 index 0000000000..eef652753d --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.5.2' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.8.0_77' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 9a687e50ddb2431600853fa58e563c3b7b54fcf1 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 17:44:10 +0200 Subject: [PATCH 0457/2403] Add easyconfig for latest PAPI version --- .../p/PAPI/PAPI-5.4.3-foss-2016a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb new file mode 100644 index 0000000000..e76514b4cc --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.3' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = [ + '3211b5a5bb389fe692370f5cf4cc2412', # papi-5.4.3.tar.gz +] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 2c9d18f3b8b4ad7726e68f266d51a22177c755d5 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:21:58 -0700 Subject: [PATCH 0458/2403] Fix source_urls for CUDA 7.0.28 --- easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index 87e535776e..ab24e09cd3 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -9,7 +9,9 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/Prod/local_installers/', +] sources = ['%(namelower)s_%(version)s_linux.run'] -- GitLab From 62c7d9239f1252566faf69b865a3107bd4c10bfb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 19:26:33 +0200 Subject: [PATCH 0459/2403] Add easyconfig for latest PDT version --- .../easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb new file mode 100644 index 0000000000..a48bf0f63e --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'PDT' +version = '3.21' + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + '3092ca0d8833b69992c17e63ae66c263', # pdtoolkit-3.21.tar.gz +] + +moduleclass = 'perf' -- GitLab From d9c5268a398def93fbee7c1ca43a024c433394b7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 14 Apr 2016 19:34:55 +0200 Subject: [PATCH 0460/2403] Add easyconfig for OPARI2 2.0 --- .../o/OPARI2/OPARI2-2.0-foss-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb new file mode 100644 index 0000000000..2f3c2cf421 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -0,0 +1,38 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +checksums = [ + '72350dbdb6139f2e68a5055a4f0ba16c', # opari2-2.0.tar.gz +] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From bb3faf23369c5cb5c69f998022a92109f0a88487 Mon Sep 17 00:00:00 2001 From: Stephane Thiell Date: Thu, 14 Apr 2016 10:42:39 -0700 Subject: [PATCH 0461/2403] cuDNN: use 5.0-rc instead of 5.0 (RC version) --- .../easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cuDNN/{cuDNN-5.0.eb => cuDNN-5.0-rc.eb} (91%) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb similarity index 91% rename from easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb rename to easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb index fcf816c8fb..536c2f33c6 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -6,7 +6,7 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '5.0' +version = '5.0-rc' homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for @@ -16,7 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-rc.tgz'] +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s.tgz'] dependencies = [('CUDA', '7.5.18')] -- GitLab From 08549d2371151ec00e4332545557bbc407b77f12 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 14:12:41 +1200 Subject: [PATCH 0462/2403] Added zlib configopt per request --- easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index 7c1a817fb6..59e0331739 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), -- GitLab From e737838f230f762c730bab0ac0c156d886cb7fb6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 10:29:05 +0800 Subject: [PATCH 0463/2403] ensure intel mpi and fft in ABINIT-7.10.5 with intel-2016.02-GCC-4.9 toolchain --- .../ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 25 +++++++++++++------ 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index d59f27574e..003543ca3f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -1,24 +1,35 @@ -# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 -# --try-toolchain=intel,2016.02-GCC-4.9, worked but it seems to at least lack mpi support +# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 +# --try-toolchain=intel,2016.02-GCC-4.9, then added intel mpi and fft support easyblock = 'ConfigureMake' name = 'ABINIT' version = "7.10.5" homepage = 'http://www.abinit.org/' -description = """ABINIT is a package whose main program allows one to find the total energy, charge density and - electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional - Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] checksums = [] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ + '--with-fft-flavor=fftw3-mkl ' \ + '--with-fft-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core"' + +# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? +# eb --try-amend can be used to install those variants from the same easyconfig file... + sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', + 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } moduleclass = 'chem' - -- GitLab From a97102970f055a0393f3c52d072bd3f55aed02cc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 15 Apr 2016 16:47:05 +1200 Subject: [PATCH 0464/2403] Update checksum --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 3ea34a9824..99e680c26d 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -14,8 +14,10 @@ source_urls = ['http://www.thch.uni-bonn.de/tc/downloads/%(name)s/data'] # tarballs with the same version number can have different checksums. For this # reason, it is suggested to manually download and rename the tarball. The # checksum may also need updating from time to time. +# Checksum last updated: 15 April 2016 +# Date tarball was reported to have been modified: 11 January 2016 sources = ['dftd3-%(version)s.tgz'] -checksums = [('md5', '88470bd398b5cc90ad680ed1df4239f7')] +checksums = [('md5', 'c9d6a92c43bb2ba71ad75f388fdce216')] files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] -- GitLab From cffac5f722257a77ce6ef8b6a705c3f67ab81d8e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:03:39 +0800 Subject: [PATCH 0465/2403] files generated with "eb Python-2.7.11-intel-2016a.eb --try-toolchain=intel,2016.02-GCC-4.9 -r" --- .../Autoconf-2.69-intel-2016.02-GCC-4.9.eb | 26 ++++ .../Automake-1.15-intel-2016.02-GCC-4.9.eb | 33 +++++ ...utotools-20150215-intel-2016.02-GCC-4.9.eb | 17 +++ .../bzip2-1.0.6-intel-2016.02-GCC-4.9.eb | 15 ++ .../g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libreadline-6.3-intel-2016.02-GCC-4.9.eb | 30 ++++ .../libtool-2.4.6-intel-2016.02-GCC-4.9.eb | 17 +++ .../m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 23 +++ .../ncurses-6.0-intel-2016.02-GCC-4.9.eb | 34 +++++ .../Python-2.7.11-intel-2016.02-GCC-4.9.eb | 139 ++++++++++++++++++ .../SQLite-3.9.2-intel-2016.02-GCC-4.9.eb | 40 +++++ .../t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb | 25 ++++ .../Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb | 26 ++++ .../zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb | 22 +++ 14 files changed, 477 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e627b672b4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..84750fffa9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..65fd1e93a3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d048641ea5 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..70b7019537 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c3f437ac8a --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..857c0faabb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b3bc79e1fe --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7c1c8c34c6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..b8a12d273e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,139 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.1.0'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%s-sse42.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..3555a7ac4c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c2af97cc03 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb new file mode 100644 index 0000000000..ed76be27b6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a389aa72f5 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From e43d75237ef71c7f231673f9c189e1bdafdf0fcf Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 15 Apr 2016 13:11:17 +0800 Subject: [PATCH 0466/2403] adapted from ASE-3.9.1.4567-intel-2016a-Python-2.7.11.eb --- ...0.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..95f2c7f4a5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.10.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['https://pypi.python.org/packages/source/a/ase/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'chem' -- GitLab From 213c16a9d14446e594d1873b334a7427e51dcf0f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 11:40:36 +0200 Subject: [PATCH 0467/2403] DB-6.2.23 for foss 2016a --- .../easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb new file mode 100644 index 0000000000..fcf1bd7696 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' \ No newline at end of file -- GitLab From 5561b2936134e5e5c2583218364d104f37419971 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 11:46:08 +0200 Subject: [PATCH 0468/2403] Drop java and add Python suffix to PostgreSQL --- ...016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgreSQL-9.5.2-intel-2016a.eb => PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index eef652753d..a7590c6580 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.5.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.mysql.com/' description = """PostgreSQL is a powerful, open source object-relational database system. @@ -20,11 +21,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} osdependencies = [('openssl-devel', 'libssl-dev')] -java = 'Java' -javaver = '1.8.0_77' - dependencies = [ - (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), -- GitLab From 9c90718ca8b5ffefc190be503c2e997aeead2c5b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Apr 2016 12:09:27 +0200 Subject: [PATCH 0469/2403] Added MADlib --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35ae5d23c5 --- /dev/null +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'MADlib' +version = '1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://madlib.incubator.apache.org' +description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] +source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('Python', '2.7.11'), + ('PostgreSQL', '9.5.2', versionsuffix), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/madpack'], + 'dirs': [] +} + +moduleclass = 'data' -- GitLab From f0a0f612b846ea753245c4d73fc78f0ea1325c99 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 13:52:48 +0200 Subject: [PATCH 0470/2403] Biopython with foss 2016a --- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..fc337c6c52 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Biopython' +version = '1.65' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://biopython.org/DIST'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, + 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ + pyshortver), + 'lib/python%s/site-packages/BioSQL' % pyshortver] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From 55e6a328a624cb037bf7a70e9d70fe3e2d8982a2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 15 Apr 2016 14:15:34 +0200 Subject: [PATCH 0471/2403] numpy dependency --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index fc337c6c52..8730db898f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -30,6 +30,7 @@ versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ (python, pyver), + ('numpy', '1.10.1', versionsuffix) ] sanity_check_paths = { -- GitLab From 9e097a1ed69abae68f558a85caa3128c44b78077 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:42:37 +0200 Subject: [PATCH 0472/2403] add easyconfig ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb, add easyconfig freetype-2.6.3-intel-2016a.eb --- .../f/freetype/freetype-2.6.3-intel-2016a.eb | 22 ++++++++ ...ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 55 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb new file mode 100644 index 0000000000..6245460dc2 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2cea64ddb8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = 'v5.34.36' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.1'), + ('Mesa', '11.1.2'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), + ('CFITSIO', '3.38'), + ('freetype', '2.6.3'), + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libXft', '2.3.2'), + ('libXpm', '3.5.11'), + ('libXext', '1.3.3'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLIBXEXT/lib' +configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' +configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' + +moduleclass = 'data' -- GitLab From 523361945d9181f98ac685afa9cebcd16a0644bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:46:28 +0200 Subject: [PATCH 0473/2403] modernise libxml2 2.9.1 easyconfig --- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb index d68ae2eaee..ae7f22f7a4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -13,15 +14,11 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic' - -pythonver = '2.7.5' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.5'), ] moduleclass = 'lib' -- GitLab From 1ac2352b2d011c437af9827b9518b29f661e467e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 14:55:52 +0200 Subject: [PATCH 0474/2403] downgrade back to freetype 2.9.3 due to conflicts in dep graph --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index 2cea64ddb8..7d1106317b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.3'), ('PCRE', '8.38'), ('CFITSIO', '3.38'), - ('freetype', '2.6.3'), + ('freetype', '2.6.2'), ('Python', '2.7.11'), ('zlib', '1.2.8'), ('libXft', '2.3.2'), -- GitLab From 88eb3bb5814e86288fa54bc8ab85b04733c72eea Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:02:06 -0400 Subject: [PATCH 0475/2403] PGI: add OpenMPI and pompi toolchain easyconfigs. --- .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 40 +++++++++++++++++++ .../easyconfigs/p/pompi/pompi-2016.03.eb | 19 +++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.03.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8cd6dea646 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.2')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +#sanity_check_commands = [ +# ('mpicc --version | grep pgcc', ''), +# ('mpicxx --version | grep pgc++', ''), +# ('mpifort --version | grep pgfortran', ''), +#] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb new file mode 100644 index 0000000000..0bf9bb7552 --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.03' +pgisuffix = '-GCC-4.9.3-2.25' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From a6b0c16f90bac68dbde7a849e551b15cce6130cb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 09:57:14 -0400 Subject: [PATCH 0476/2403] PGI: add pomkl-2016.03 toolchain + imkl-11.3.2.181-pompi + HPL --- .../h/HPL/HPL-2.1-pomkl-2016.03.eb | 23 ++++++++++++ .../i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 36 +++++++++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.03.eb | 20 +++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb new file mode 100644 index 0000000000..73bc06cddb --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -0,0 +1,23 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.03'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +# needs to include -ldl or else we get +# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' +import os +os.environ['LIBS'] = '-ldl' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb new file mode 100644 index 0000000000..ac3a95728c --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.2.181' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'pompi', 'version': '2016.03'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb new file mode 100644 index 0000000000..6b7d80bf52 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.03' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.3' +gccsuff = '-GCC-4.9.3-2.25' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.2.181', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' -- GitLab From dc578361e24586f76539339d6624d11163d73cfb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 15 Apr 2016 10:27:01 -0400 Subject: [PATCH 0477/2403] Move checksum under sources. --- .../easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb index e54c32859f..91b7fa73b1 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.3.eb @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'numactl' version = '2.0.11' -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - homepage = 'http://oss.sgi.com/projects/libnuma/' description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. @@ -15,6 +13,8 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + builddependencies = [('binutils', '2.25')] sanity_check_paths = { -- GitLab From 63e171985e5db8c4347f3689c19e473fb2302667 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Apr 2016 22:34:37 +0200 Subject: [PATCH 0478/2403] add easyconfig Singularity-1.0-GCC-4.9.3-2.25.eb --- .../Singularity-1.0-GCC-4.9.3-2.25.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8d785f5395 --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '1.0' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/sapprun', 'bin/singularity'], + 'dirs': ['libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From 80fdf0a80881156c27cf8f1758b4fa29498ec00e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:10:04 +0800 Subject: [PATCH 0479/2403] removed empty checksums line --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 003543ca3f..457e0344c7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -16,7 +16,6 @@ toolchainopts = {'usempi': True} source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] -checksums = [] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ -- GitLab From 4699a7ded9ba555502560808128af5ff10ff9ef7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:31:45 +0800 Subject: [PATCH 0480/2403] use --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 457e0344c7..670f55a3aa 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -20,7 +20,7 @@ sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core"' + '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... -- GitLab From 2d346147e65a1c386ed640277af77b2570fb42a6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:32:31 +0800 Subject: [PATCH 0481/2403] drop initial comments --- .../easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 670f55a3aa..56d9801a74 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,3 @@ -# initially generated with eb ABINIT-7.10.4-intel-2015a.eb --try-software-version=7.10.5 -# --try-toolchain=intel,2016.02-GCC-4.9, then added intel mpi and fft support easyblock = 'ConfigureMake' name = 'ABINIT' -- GitLab From 1cc58270bcf50313de5768625c59b4bdfa7a910e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:33:55 +0800 Subject: [PATCH 0482/2403] fix code style --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 56d9801a74..ebe9e262ac 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -18,14 +18,13 @@ sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="$LIBFFT"' + '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', - 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 79992eb03a7801afb1cfb8775b8082eb86d49e9f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:45:14 +0800 Subject: [PATCH 0483/2403] fix code style --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index ebe9e262ac..049507e41f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -16,9 +16,9 @@ source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] # ensure mpi and intel toolchain -configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' \ - '--with-fft-flavor=fftw3-mkl ' \ - '--with-fft-libs="$LIBFFT"' +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT"' # there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? # eb --try-amend can be used to install those variants from the same easyconfig file... -- GitLab From ea458d6c6e4761e35835c3a85f1b25894dc9eab0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:54:18 +0800 Subject: [PATCH 0484/2403] add CPPFLAGS=-fgnu89-inline to M4 eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index b3bc79e1fe..899804b18f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 2a5b19d02f135381c0d70b5bddb092400cc9a867 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 07:55:24 +0800 Subject: [PATCH 0485/2403] use env in libreadline eb --- .../l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb index c3f437ac8a..9c5b9b6279 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "LDFLAGS='-lncurses'" +preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 21ad457a50367bae49fcabae0713cddf08c4fcfa Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:01:55 +0800 Subject: [PATCH 0486/2403] use pyver template --- .../ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 95f2c7f4a5..3592b22134 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ASE' version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://wiki.fysik.dtu.dk/ase/' description = """ASE is a python package providing an open source Atomic Simulation Environment @@ -12,17 +13,15 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = ['https://pypi.python.org/packages/source/a/ase/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] sanity_check_paths = { 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'chem' -- GitLab From 4a9dbd98c864d90586d41615b289cb2b617d348d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:03:41 +0800 Subject: [PATCH 0487/2403] use PYPI_LOWER_SOURCE and SOURCELOWER_TAR_GZ --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 3592b22134..96dd7193cd 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -10,8 +10,8 @@ description = """ASE is a python package providing an open source Atomic Simulat toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -source_urls = ['https://pypi.python.org/packages/source/a/ase/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] versionsuffix = '-Python-%s' % pyver -- GitLab From 559166337d94b390123c8fd3858e990479bb3851 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 08:05:29 +0800 Subject: [PATCH 0488/2403] remove duplicated versionsuffix --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 96dd7193cd..ca4b5697db 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -versionsuffix = '-Python-%s' % pyver - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From d1ac97c1d17a194f4da66b1863e98566298b9a5b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 16 Apr 2016 15:01:14 +0800 Subject: [PATCH 0489/2403] add variant with libxc support --- ...INIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb new file mode 100644 index 0000000000..113a1ca853 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = "7.10.5" +versionsuffix = "_libxc" + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# ensure mpi and intel toolchain +configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' +configopts += '--with-fft-flavor=fftw3-mkl ' +configopts += '--with-fft-libs="$LIBFFT" ' + +# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? +# eb --try-amend can be used to install those variants from the same easyconfig file... + +# libxc variant +configopts += '--with-dft-flavor=libxc ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From ec81d7170848d183f52d41ddb7ed37146662f282 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 15:47:40 +0200 Subject: [PATCH 0490/2403] Add easyconfig for Cube 4.3.4 --- .../c/Cube/Cube-4.3.4-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb new file mode 100644 index 0000000000..2ac3b5a935 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Cube' +version = '4.3.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '50f73060f55311cb12c5b3cb354d59fa', # cube-4.3.4.tar.gz +] + +dependencies = [ + ('Qt', '4.8.7'), +] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), + ("lib/libcube4.%s" % SHLIB_EXT, "lib64/libcube4.%s" % SHLIB_EXT)], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From bd7a5f04e9f9fc8c4125d84c29da5cdec5bbf590 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 15:57:14 +0200 Subject: [PATCH 0491/2403] Add easyconfig for OTF2 2.0 --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb new file mode 100644 index 0000000000..42ee5fa840 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -0,0 +1,38 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib/libotf2.a", "lib64/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 08d30a3a12bdcc7a0e31d1a478ec81ea6cedd253 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 17:31:31 +0200 Subject: [PATCH 0492/2403] Add easyconfig for Score-P 2.0.1 --- .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb new file mode 100644 index 0000000000..1657f1511e --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '2.0.1' + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['scorep-%(version)s.tar.gz'] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +checksums = [ + '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz +] + +dependencies = [ + # binutils is implicitly available via GCC toolchain + # ('binutils', '2.25', '', ('GCCcore', '4.9.3')), + ('Cube', '4.3.4'), + ('OPARI2', '2.0'), + ('OTF2', '2.0'), + ('PAPI', '5.4.3'), + ('PDT', '3.21'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib/libscorep_adapter_mpi_event.a", "lib64/libscorep_adapter_mpi_event.a"), + ("lib/libscorep_adapter_mpi_event.%s" % SHLIB_EXT, "lib64/libscorep_adapter_mpi_event.%s" % SHLIB_EXT)], + 'dirs': [], +} + +# Ensure that local metric documentation is found by Cube GUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' -- GitLab From d9bbb9563527681c5ae947bd520e25ff1cadf9ea Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 16 Apr 2016 17:42:07 +0200 Subject: [PATCH 0493/2403] Fix packmol eb and add newest version --- .../p/packmol/packmol-13.243-ictce-4.1.13.eb | 4 ++-- .../p/packmol/packmol-16.103-intel-2016a.eb | 23 +++++++++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb index 29c565eb8d..669406175c 100644 --- a/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/packmol/packmol-13.243-ictce-4.1.13.eb @@ -3,13 +3,13 @@ easyblock = "MakeCp" name = 'packmol' version = '13.243' -homepage = 'http://www.cmbi.ru.nl/molden/' +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' description = "Packing Optimization for Molecular Dynamics Simulations" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['https://packmol.googlecode.com/files'] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] buildopts = 'FORTRAN="$F90"' diff --git a/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb new file mode 100644 index 0000000000..a5ed58eedd --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-16.103-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = "MakeCp" + +name = 'packmol' +version = '16.103' + +homepage = 'http://www.ime.unicamp.br/~martinez/packmol/' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://leandro.iqm.unicamp.br/packmol/versionhistory'] + +buildopts = 'FORTRAN="$F90"' + +files_to_copy = [(['packmol'], 'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/packmol', 'COPYING', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From fdf27805329e819e54f906f4f8d0efc4ad1298ab Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sat, 16 Apr 2016 18:29:22 +0200 Subject: [PATCH 0494/2403] Add easyconfig for Scalasca 2.3 --- .../s/Scalasca/Scalasca-2.3-foss-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb new file mode 100644 index 0000000000..250c8ea829 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb @@ -0,0 +1,45 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.3' + +homepage = 'http://www.scalasca.org/' +description = """Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The analysis identifies + potential performance bottlenecks -- in particular those concerning communication and + synchronization -- and offers guidance in exploring their causes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + 'de782c8b6ecfce0e16a4b143ba7a9b5a', # scalasca-2.3.tar.gz +] + +dependencies = [ + ('Cube', '4.3.4'), + ('OTF2', '2.0'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib/libpearl.replay.a", "lib64/libpearl.replay.a")], + 'dirs': [], +} + +# Ensure that local metric documentation is found by Cube GUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' -- GitLab From 2bd9fac7ab90a4cb83e0a5c77cfd85273eb56e91 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 14:11:16 -0400 Subject: [PATCH 0495/2403] Using %(pyver)s and %(pyshortver)s template for ScientificPython and numpy easyconfig --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 8 +++----- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 9 +++------ 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index e591de8fe1..eeb3a0e326 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -13,14 +13,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.8.1-mkl.patch'] +versionsuffix = '-Python-%(pyver)s' -python = 'Python' -pyver = '2.7.11' -versionsuffix = '-%s-%s' % (python, pyver) +patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index ef29eaf445..c1b4e8f39a 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -13,13 +13,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), # older version of numpy than the one included in Python module required # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for ('numpy', '1.8.2', versionsuffix), @@ -29,7 +26,7 @@ options = {'modulename': 'Scientific'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/Scientific' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'], } moduleclass = 'math' -- GitLab From ee958027b6ebcc5c2ee4a0161c16e773e52aa5f9 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Sat, 16 Apr 2016 15:02:52 -0400 Subject: [PATCH 0496/2403] adjust position versionsuffix --- .../n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb | 3 +-- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb index eeb3a0e326..b9ddbc1927 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'numpy' version = '1.8.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.numpy.org' description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: @@ -13,8 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - patches = ['numpy-1.8.1-mkl.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index c1b4e8f39a..1c40ab4f4d 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'ScientificPython' version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' description = """ScientificPython is a collection of Python modules for scientific computing. @@ -13,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' dependencies = [ ('Python', '2.7.11'), -- GitLab From f2412f0594a35ca854a7aa07266a8278ef60fb4a Mon Sep 17 00:00:00 2001 From: jrbosch Date: Sat, 16 Apr 2016 15:05:37 -0400 Subject: [PATCH 0497/2403] Update ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb --- .../ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index 1c40ab4f4d..267282ee97 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), # older version of numpy than the one included in Python module required -- GitLab From 7f3237cc029b0d1f089f80a06e6f764807f8e8f7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 16:16:22 +0200 Subject: [PATCH 0498/2403] preinstall opts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b280622820..efd22bd922 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,6 +3,9 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' +preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' + + homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -14,7 +17,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Perl', '5.22.1'), - ('DB', '4.8.30'), + ('DB', '6.2.23'), ] sanity_check_paths = { -- GitLab From b2ba3820d14534216925834905539bb6153994b9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 17 Apr 2016 17:25:37 +0200 Subject: [PATCH 0499/2403] Bowtie with foss 2016a --- .../b/Bowtie/Bowtie-1.1.2-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb new file mode 100644 index 0000000000..7979ba4e23 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-foss-2016a.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From 0e80dac7141e79a117e7674230156c9f66204fc1 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 12:36:43 +1200 Subject: [PATCH 0500/2403] New EasyConfig for binutils 2.26 with the GCC core 4.9.2 --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..75c194bc7b --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c6e1b054ff4644003954ba0dbe6ac7dab8a525d9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:25:07 +1200 Subject: [PATCH 0501/2403] New EasyConfig for binutils 2.25 with GCC core 4.9.2 --- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a9d4815d89 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + + ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a0283d931e8b0133cca0e511484f4ddb825824d0 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:29:50 +1200 Subject: [PATCH 0502/2403] New EasyConfig for zlib with the GCCcore 4.9.2 compiler --- .../z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..a7b3977bb9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 74fa24f980d83f4c0bfed691b837d5137a807a0d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:30:25 +1200 Subject: [PATCH 0503/2403] New EasyConfig for the GCC core -- GCC 4.9.2 compiler --- .../easyconfigs/g/GCCcore/GCCcore-4.9.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb new file mode 100644 index 0000000000..01f4776c64 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '4.9.2' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' +gcc_name = 'GCC' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + '%s-%s.tar.bz2' % (gcc_name.lower(), version), + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From 1d9edaed048b05f78f4c52c6c7e8b8985cd9dcd5 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:36:06 +1200 Subject: [PATCH 0504/2403] New EasyConfig for flex 2.5.39 with the GCCcore 4.9.2 toolchain --- .../f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..71675a8b5c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.25', '', True) +] + +moduleclass = 'lang' -- GitLab From f0a867d2f56b99b4233ad60709796e966a1d9db7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:40:26 +1200 Subject: [PATCH 0505/2403] New EasyConfig for M4 1.4.17 with the GCCcore 4.9.2 toolchain --- .../m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..5551b81d85 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6b51bde2d6ac315665b0bfe4c83df85a81bbd617 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:29:53 +1200 Subject: [PATCH 0506/2403] New EasyConfig for Bison 3.0.4 with the GCCcore 4.9.2 toolchain --- .../b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..159751eac5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From f055ab3a57d7eea9846742e9507bfc302ec8db05 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 15:39:05 +1200 Subject: [PATCH 0507/2403] New EasyConfig for numactl 2.0.11 with the GCCcore toolchain --- .../n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb new file mode 100644 index 0000000000..49ba8f9bf3 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.2'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.25')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From d5737cc4992c7571f25173d5cabd1b68e76560d5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 15:20:26 +0800 Subject: [PATCH 0508/2403] initial commit for BerkeleyGW-1.0.6 using intel-2016.02-GCC-4.9 toolchain (not working) --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6b0669dd87 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.0.6" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['8740562da41e87a62eb8d457675e4bfd'] + +files_to_copy = ['*'] + +prebuildopts = 'touch arch.mk; ' + +buildopts = 'all-flavors' + +parallel = 1 -- GitLab From 39fe8799dc0bf5b5332674dc40ea04a4b452d54c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:02:22 +0200 Subject: [PATCH 0509/2403] Bonnie++ with foss 2016a --- .../b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb new file mode 100644 index 0000000000..4d9f9e29d3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '1.97' + +homepage = 'http://www.coker.com.au/bonnie++/' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://www.coker.com.au/bonnie++/experimental'] + +toolchain = {'name': 'foss', 'version': '2016a'} + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +moduleclass = 'tools' + -- GitLab From b1c9ec39190cbd12d599b1f0df233e09bb29d230 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:25:51 +0200 Subject: [PATCH 0510/2403] remove DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 23b49aa5020cb896337ae7875a886c2d51b0456d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 10:27:59 +0200 Subject: [PATCH 0511/2403] removed DB eb file --- .../easyconfigs/d/DB/DB-4.8.30-foss2016a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb b/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb deleted file mode 100644 index 0db26d6d7e..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-4.8.30-foss2016a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '4.8.30' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://download.oracle.com/berkeley-db/'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/db.h', 'include/db_cxx.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], - 'dirs': ['bin'], -} - -moduleclass = 'tools' -- GitLab From 9a01d8b691c5da8fdda8188a18eb4a83458bb119 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 11:23:40 +0200 Subject: [PATCH 0512/2403] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index efd22bd922..19d6de4aa0 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -3,7 +3,6 @@ easyblock = 'PerlModule' name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' -preinstallopts = 'export DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib' @@ -20,6 +19,8 @@ dependencies = [ ('DB', '6.2.23'), ] +preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' + sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], 'dirs': [], -- GitLab From 29a97dd8e9370b38c0947ec500a17f4ef87b2997 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Apr 2016 17:24:34 +0800 Subject: [PATCH 0513/2403] initial support of Wannier90-1.2 and 2.0.1 with intel-2016.02-GCC-4.9 --- .../Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 25 ++++++++++++++++++ .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 26 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..71d744077f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '1.2' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..e7a229fa5e --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +# ugly hack +prebuildopts = 'rm make.sys; touch make.sys; ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 6e96e854e1786abe3f0676ea977c038f95fe4f5f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 12:58:45 +0200 Subject: [PATCH 0514/2403] export path --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 19d6de4aa0..b03011fb99 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -4,8 +4,6 @@ name = 'DB_File' version = '1.835' versionsuffix = '-Perl-%(perlver)s' - - homepage = 'http://perldoc.perl.org/DB_File.html' description = """Perl5 access to Berkeley DB version 1.x.""" @@ -19,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'export DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" && ' +preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], @@ -27,3 +25,4 @@ sanity_check_paths = { } moduleclass = 'data' + -- GitLab From 8a14112aef54d4ff60bfdc915e2ef1c573862fe4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:15:33 +0200 Subject: [PATCH 0515/2403] preconfigopts --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index b03011fb99..85e0ba3145 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preinstallopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From e54a2cf119497b7be7322575ab5e5d7bc7efb450 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Apr 2016 13:17:23 +0200 Subject: [PATCH 0516/2403] brackets --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 85e0ba3145..326da3c949 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ' +preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 281ca1e55eba6725c38c3908d3a9f79d7c294769 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 13:45:40 +0200 Subject: [PATCH 0517/2403] Add easyconfigs for SIONlib (regular and tools) --- .../SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 41 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.6.1-foss-2016a.eb | 37 +++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb new file mode 100644 index 0000000000..b8509256ef --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + '57208e08309cf8892fe3daee90567d21', # sionlib-1.6.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb new file mode 100644 index 0000000000..a093e042cb --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.6.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '47113ebc00ae38c4f0965659427a0242', # sionlib-1.6.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From 0b8a1d171cd8ce4edcb8f45412d367407593a480 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 14:28:25 +0200 Subject: [PATCH 0518/2403] Add foss/2016a easyconfig for libunwind 1.1 Enable libunwind support for Score-P --- .../l/libunwind/libunwind-1.1-foss-2016a.eb | 27 +++++++++++++++++++ .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 1 + 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb new file mode 100644 index 0000000000..9583401685 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 1657f1511e..66303634bd 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -31,6 +31,7 @@ checksums = [ dependencies = [ # binutils is implicitly available via GCC toolchain # ('binutils', '2.25', '', ('GCCcore', '4.9.3')), + ('libunwind', '1.1'), ('Cube', '4.3.4'), ('OPARI2', '2.0'), ('OTF2', '2.0'), -- GitLab From 7e8ab8b214515ea6b6eaf46ee43d5fcade48778a Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 14:54:42 +0200 Subject: [PATCH 0519/2403] Add SIONlib as a build dependency --- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 42ee5fa840..3b724d990f 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -28,6 +28,8 @@ checksums = [ '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz ] +builddependencies = [('SIONlib', '1.6.1', '-tools')] + configopts = '--enable-shared' sanity_check_paths = { -- GitLab From aaee1240312cea617f9b801a5f04aaaa4c0cb7e4 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 18 Apr 2016 15:27:53 +0200 Subject: [PATCH 0520/2403] As requested, comment on the tools version --- .../easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb index b8509256ef..e773779617 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -10,6 +10,8 @@ easyblock = 'ConfigureMake' name = 'SIONlib' version = '1.6.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details versionsuffix = '-tools' homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' -- GitLab From 9cca4fb7a7bde5cc26ae1676c8bae8ef71ca0b3f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 13:33:17 -0400 Subject: [PATCH 0521/2403] add IPython 3.2.3 easyconfig for foss 2016a toolchain --- .../IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 85 +++++++++++++++++++ .../l/libsodium/libsodium-1.0.8-foss-2016a.eb | 20 +++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb | 27 ++++++ ...MQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb | 29 +++++++ .../util-linux-2.27.1-foss-2016a.eb | 33 +++++++ .../z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb | 35 ++++++++ 6 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..02467990c5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,85 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb new file mode 100644 index 0000000000..ef8bb83cbf --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.8' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb new file mode 100644 index 0000000000..5f92dedd69 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000..c279b32410 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.2.0-foss-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.2.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +dependencies = [ + ('Python', '2.7.11'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb new file mode 100644 index 0000000000..6e398ddd1e --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.27.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb new file mode 100644 index 0000000000..c67d70fb3a --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.4-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.4' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.27.1'), + ('libsodium', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 832b44908ab598ddc706fcd9b75c51e5f3d9103f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:04:21 -0400 Subject: [PATCH 0522/2403] add Eigen 3.2.7 for foss 2016a --- .../easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb new file mode 100644 index 0000000000..a45d43c1fa --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.7' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 2695a9a0755c6dc34e0df8aa241c928479718f44 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Mon, 18 Apr 2016 17:53:55 -0400 Subject: [PATCH 0523/2403] include MarkupSafe 0.23 in exts_list --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index 02467990c5..f70668f24c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -48,6 +48,9 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), -- GitLab From 0586ff6d4fcacfd2c8d8b8135c9837d5e2fce4f2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 07:04:59 +0800 Subject: [PATCH 0524/2403] fix prebuildopts --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 71d744077f..5359496146 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e7a229fa5e..631f9e28bc 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,8 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="-O2" LDOPTS="-O2" LIBDIR=$LAPACK_LIB_DIR LIBS=$LIBLAPACK ' +prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From b5def49e41686976750ad72b309f87a423364a69 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 19 Apr 2016 13:45:29 +1200 Subject: [PATCH 0525/2403] Removed binutils-2.26 as it is untested and unneeded --- .../b/binutils/binutils-2.26-GCCcore-4.9.2.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb deleted file mode 100644 index 75c194bc7b..0000000000 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-4.9.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'binutils' -version = '2.26' - -homepage = 'http://directory.fsf.org/project/binutils/' -description = "binutils: GNU binary utilities" - -toolchain = {'name': 'GCCcore', 'version': '4.9.2'} - -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - -builddependencies = [ - ('M4', '1.4.17'), - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) -] - -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 51f553d9979e251dbf093b75ca12bb52fa5006c3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:16:10 +0800 Subject: [PATCH 0526/2403] replace hardcoded ifort with $F90 --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 2 +- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 5359496146..73eeb08ff4 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x'], 'bin')] diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index 631f9e28bc..e4b353566b 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.wannier.org/code'] # ugly hack prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=ifort COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] -- GitLab From 6a9ae05c1350d30f21dbf43ec17c7d7b2fc378f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 09:34:51 +0200 Subject: [PATCH 0527/2403] clean up Tau easyconfig w.r.t. Tau easyblock --- .../t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb | 110 +++--------------- 1 file changed, 13 insertions(+), 97 deletions(-) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb index 008012a78d..aef14769f2 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb @@ -6,113 +6,29 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -import platform - -name = "TAU" -version = "2.22.2" -# --- BM ISSUE --- -# -# Use hardcoded x86_64 here? -machine = platform.machine() +name = 'TAU' +version = '2.22.2' homepage = 'http://tau.uoregon.edu' description = """The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {"usempi": True} - -compname = 'GCC' -compver = '4.7.3' - -# compiler toolchain depencies -dependencies = [ - ('OTF', '1.12.4', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), - ('PDT', '3.19', "", (compname, compver)), - #('Scalasca', '1.4.3'), # requires enabling scalasca1 as extra backend - #('Score-P', '1.2.1'), # requires enabling scorep as extra backend - ('VampirTrace', '5.14.4'), # requires enabling vampirtrace as extra backend -] - -extra_backends = [ - #'scalasca1', # deprecated, use scorep backend instead (requires Scalasca v1.x as dependency) - #'vampirtrace', # deprecated, use scorep backend instead (requires VampirTrace as dependency) - 'scorep', # requires Score-P as dependency -] +toolchainopts = {'usempi': True} -# http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.22.2.tar.gz -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] +sources = [SOURCELOWER_TAR_GZ] -# --- BM CONFIGOPTS --- -# -# Compiler should always be specified -- MUCH quicker and SAVER than autodetect -# -c++=[CC|KCC|g++|*xlC*|cxx|pgCC|pgcpp|FCC|guidec++|aCC|c++|ecpc| -# clang++|bgclang++|g++4|icpc|scgcc|scpathCC|pathCC|orCC] -# -cc=[cc|gcc|clang|bgclang|gcc4|scgcc|KCC|pgcc|guidec|*xlc*|ecc|pathcc|orcc] -# -fortran=[gnu|sgi|ibm|ibm64|hp|cray|pgi|absoft|fujitsu|sun|compaq|g95| -# open64|kai|nec|hitachi|intel|absoft|lahey|nagware|pathscale|gfortran|gfortran4] - -# Basic config: compiler, OpenMP, MPI -compcfgopts = ' -cc=gcc -c++=g++ -fortran=gfortran4' -ompcfgopts = ' -opari' -mpicfgopts = ' -mpiinc=${EBROOTOPENMPI}/include -mpilib=${EBROOTOPENMPI}/lib64' - -# Optional extra modes config: -scacfgopts = ' -scalasca=${EBROOTSCALASCA}' -vtcfgopts = ' -vampirtrace=${EBROOTVAMPIRTRACE}' -scocfgopts = ' -scorep=${EBROOTSCOREMINP}' - -# Optional packages config: -pdtcfgopts = ' -pdt=${EBROOTPDT}' -papicfgopts = ' -papi=${EBROOTPAPI}' -optionalcfgs = pdtcfgopts + papicfgopts # + otfcfgopts -# --- BM ISSUE --- -# -# TAU cannot handle name changes yet introduced with OTF-1.12.3 -#otfcfgopts = ' -otf=${EBROOTOTF}' - -# TAU special build procedure -prefix_opt = '-prefix=' -installopts = 'clean' -keeppreviousinstall = True -skipsteps = ['build'] - -# TAU build: Configure + make install for each combination of modes defined above -configopts = [ - # Basic TAU mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+optionalcfgs, - compcfgopts+ompcfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+optionalcfgs, - # Scalasca mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+scacfgopts+optionalcfgs, - compcfgopts+ompcfgopts+scacfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+scacfgopts+optionalcfgs, - # Vampirtrace mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+vtcfgopts+optionalcfgs, - compcfgopts+ompcfgopts+vtcfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+vtcfgopts+optionalcfgs, - # Score-P mode + MPI, OMP, OMPI - compcfgopts+mpicfgopts+scocfgopts+optionalcfgs, - compcfgopts+ompcfgopts+scocfgopts+optionalcfgs, - compcfgopts+mpicfgopts+ompcfgopts+scocfgopts+optionalcfgs, +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), + ('Scalasca', '1.4.3'), + ('Score-P', '1.2.1'), + ('VampirTrace', '5.14.4'), ] -sanity_check_paths = { - 'files': [machine + "/bin/pprof", "include/TAU.h", machine + "/lib/libTAU.so"], - 'dirs': [] -} - - -# default measurement settings -modextravars = { - 'TAU_MAKEFILE': '%(installdir)s/lib/Makefile.tau-papi-mpi-pdt', - 'TAU_PROFILE': '1', - 'TAU_TRACE': '0', - 'TAU_CALLPATH': '1', - 'TAU_CALLPATH_DEPTH': '10', - 'TAU_COMM_MATRIX': '1', -} +# scalasca and vampirtrace backends are deprecated +extra_backends = ['scalasca', 'scorep', 'vampirtrace'] moduleclass = 'perf' -- GitLab From 5ee511dc03e1383691dcf9ce3ce7740a5b091115 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:39:45 +0800 Subject: [PATCH 0528/2403] also build and install library --- .../w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 7 +++++-- .../w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index 73eeb08ff4..a1e273882c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -15,10 +15,13 @@ source_urls = ['http://www.wannier.org/code'] prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x'], 'bin')] +# build program and library +buildopts = 'all' + +files_to_copy = [(['wannier90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x'], + 'files': ['bin/wannier90.x', 'lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index e4b353566b..c85a2e8e7c 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -17,10 +17,13 @@ prebuildopts = 'rm make.sys; touch make.sys; ' prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin')] +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x'], + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], 'dirs': [] } -- GitLab From e806c6cde1ebae19b1f2a0083b8f67086b65f01f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 09:42:51 +0200 Subject: [PATCH 0529/2403] clean up VampirTrace easyconfig --- ...VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb | 74 +++++++------------ 1 file changed, 26 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb index 304ad188de..7e266eb32f 100644 --- a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb @@ -1,71 +1,49 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD # # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -name = "VampirTrace" -version = "5.14.4" +easyblock = 'ConfigureMake' + +name = 'VampirTrace' +version = '5.14.4' homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' description = """VampirTrace is an open source library that allows detailed logging of program - execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). - Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated - applications and generates exact time stamps for all GPU related events. - Additional highlights are I/O event and memory allocation tracing as well as recording of counter metrics - like PAPI and external counters. - VampirTrace provides several variants to instrument the application source code, such as manual, automatic - by the compiler, binary (Dyninst) instrumentation and library wrapping. - The log data is written in the Open Trace Format (OTF), which can be analyzed and visualized by the visualization tool Vampir. - VampirTrace has established a wide user base and has become an integral part of Open MPI version 1.3 and higher.""" + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} -toolchainopts = {"usempi": True} +toolchainopts = {'usempi': True} -compname = 'GCC' -compver = '4.7.3' +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] -# compiler toolchain depencies dependencies = [ - ('OTF', '1.12.4', "", (compname, compver)), - ('PAPI', '5.2.0', "", (compname, compver)), - ('PDT', '3.19', "", (compname, compver)), + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), ] -# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz -sources = [SOURCE_TAR_GZ] -source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] +configopts = 'MPIFC="$MPIF90"' -# --- BM CONFIGOPTS --- -# # MPI suite should always be specified -- MUCH quicker and SAVER than autodetect -# --with-hpmpi | --with-pcmpi | --with-intelmpi | --with-intelmpi2 | --with-lam | --with-mpibgl | --with-mpibgp | -# --with-mpibgq | --with-mpich | --with-mpich2 | --with-mvapich | --with-mvapich2 | --with-mpisx | --with-mpisx-ew | -# --with-openmpi | --with-openmpi17 | --with-sgimpt | --with-sunmpi | --with-sunmpi-mt | --with-mpibull2 -# -# --- BM ISSUE --- -# -# MPIxx variable settings and --enable-compinst= options are ToolChain specific!!! -configopts = ' MPIFC=mpif90' -configopts += ' --with-openmpi' # quicker and saver than autodetect -configopts += ' --enable-compinst=gnu' -configopts += ' --with-papi-dir=${EBROOTPAPI}' -configopts += ' --with-extern-otf-dir=${EBROOTOTF}' -configopts += ' --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor' -configopts += ' --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse' -configopts += ' --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse' -configopts += ' --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse' -# --- BM EXTENSIONS --- -# -# VamoirTrace does also support CUDA measurements - not yet tested in EasyBuild -# configopts += ' --with-cuda-dir=${CUDADIR}' +# note: these options are toolchain specific! +configopts += " --with-openmpi --enable-compinst=gnu" + +configopts += " --with-papi-dir=${EBROOTPAPI}" +configopts += " --with-extern-otf-dir=${EBROOTOTF}" +configopts += " --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor" +configopts += " --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse" +configopts += " --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse" +configopts += " --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse" +# VamoirTrace does also support CUDA measurements - not yet tested +# configopts += " --with-cuda-dir=${CUDADIR}" -# --- BM LIB64 --- -# -# On some systems libraries end up in lib/ sanity_check_paths = { - 'files': ["bin/vtcc", "include/vampirtrace/vt_user.h", "lib64/libvt.a"], + 'files': ['bin/vtcc', 'include/vampirtrace/vt_user.h', ('lib/libvt.a', 'lib64/libvt.a')], 'dirs': [] } -- GitLab From 0332209ac50434cc5c4839baf8e2b627403ba653 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 15:53:41 +0800 Subject: [PATCH 0530/2403] replace ugly hack with patch --- .../Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb | 6 +++--- .../Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../w/Wannier90/Wannier90_1x_ignore_makesys.patch | 11 +++++++++++ .../w/Wannier90/Wannier90_2x_ignore_makesys.patch | 11 +++++++++++ 4 files changed, 28 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb index a1e273882c..e92974ac88 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-1.2-intel-2016.02-GCC-4.9.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +patches = ['Wannier90_1x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library buildopts = 'all' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb index c85a2e8e7c..acef4f4eb1 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016.02-GCC-4.9.eb @@ -12,9 +12,9 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.wannier.org/code'] -# ugly hack -prebuildopts = 'rm make.sys; touch make.sys; ' -prebuildopts += 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' # build program and library diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch new file mode 100644 index 0000000000..66cb495806 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 ++++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../make.sys ++#include ../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch new file mode 100644 index 0000000000..fa4a6de14a --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -0,0 +1,11 @@ +--- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 ++++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 +@@ -1,7 +1,7 @@ + # Should be no need to change below this line + # + +-include ../../make.sys ++#include ../../make.sys + + OBJS = constants.o io.o utility.o parameters.o hamiltonian.o overlap.o \ + kmesh.o disentangle.o wannierise.o plot.o transport.o -- GitLab From 00d86c4a4a52e9768716016aa6ab8b2718d6a3c0 Mon Sep 17 00:00:00 2001 From: jgp Date: Tue, 19 Apr 2016 09:58:35 +0200 Subject: [PATCH 0531/2403] PGI: adding Cray's PrgEnv-pgi --- .../easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb new file mode 100644 index 0000000000..5de532fe82 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -0,0 +1,21 @@ +easyblock = 'CrayToolchain' + +name = 'CrayPGI' +version = '2016.04' + +homepage = 'http://www.pgroup.com/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + # ('PrgEnv-pgi/' + version, EXTERNAL_MODULE), + ('PrgEnv-pgi/5.2.82', EXTERNAL_MODULE), + ('pgi/16.3.0' , EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), + # ('cray-libsci/16.03.1', EXTERNAL_MODULE), # Cray does not provide cray-libsci for PrgEnv-pgi +] + +moduleclass = 'toolchain' + -- GitLab From fc2e6ea513107ef4f1dc1e1f88f8757720e52341 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 10:31:14 +0200 Subject: [PATCH 0532/2403] stick to gompi/1.4.12-no-OFED, for which deps are already available --- ...mpi-1.5.12-no-OFED.eb => TAU-2.22.2-gompi-1.4.12-no-OFED.eb} | 2 +- ...12-no-OFED.eb => VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/TAU/{TAU-2.22.2-gompi-1.5.12-no-OFED.eb => TAU-2.22.2-gompi-1.4.12-no-OFED.eb} (94%) rename easybuild/easyconfigs/v/VampirTrace/{VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb => VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb} (96%) diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb index aef14769f2..5632c4ca09 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb @@ -13,7 +13,7 @@ homepage = 'http://tau.uoregon.edu' description = """The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'usempi': True} source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb similarity index 96% rename from easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb index 7e266eb32f..02bc1f21cc 100644 --- a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb @@ -15,7 +15,7 @@ homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' description = """VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" -toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'usempi': True} sources = [SOURCE_TAR_GZ] -- GitLab From 449cc75fd5e13863595ea0e308c1b36c3d644962 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 19 Apr 2016 17:52:05 +0800 Subject: [PATCH 0533/2403] add explanatory comments to patch files --- .../easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch | 2 ++ .../easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch index 66cb495806..07fb605587 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_1x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.orig 2016-04-19 15:26:27.373047000 +0800 +++ src/Makefile 2016-04-19 15:26:32.414229150 +0800 @@ -1,7 +1,7 @@ diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch index fa4a6de14a..8bf5e9aa01 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_2x_ignore_makesys.patch @@ -1,3 +1,5 @@ +avoid including make.sys, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.2.orig 2016-04-19 15:29:17.248672000 +0800 +++ src/Makefile.2 2016-04-19 15:29:21.648448096 +0800 @@ -1,7 +1,7 @@ -- GitLab From 777c8581b0c4d9f63871586b1a28ff6d0f39fc61 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:21:08 +0200 Subject: [PATCH 0534/2403] removed newline --- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb index 4d9f9e29d3..f63a76fa69 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -26,4 +26,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From 5ae36bfe05d535e1d664cd00d5bb0747a4eb051d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 19 Apr 2016 14:22:53 +0200 Subject: [PATCH 0535/2403] use of env --- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 326da3c949..8c069fec94 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('DB', '6.2.23'), ] -preconfigopts = 'DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], -- GitLab From 7010b4032c4c42ea200bdcc329aa738a607c5863 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:04:01 +0200 Subject: [PATCH 0536/2403] add easyconfig LLVM-3.8.0-intel-2016a.eb, add easyconfig CMake-3.5.2-intel-2016a.eb --- .../c/CMake/CMake-3.5.2-intel-2016a.eb | 31 +++++++++++++++ .../l/LLVM/LLVM-3.8.0-intel-2016a.eb | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb new file mode 100644 index 0000000000..6d07f31ebd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb new file mode 100644 index 0000000000..1aa8a611cd --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.1'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 2f12335cd3d739900ac625cc64cee51876236104 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 15:08:40 +0200 Subject: [PATCH 0537/2403] modify easyconfig LLVM-3.8.0-intel-2016a.eb --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb index 1aa8a611cd..7a9543d260 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-intel-2016a.eb @@ -28,9 +28,11 @@ dependencies = [ ] configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" sanity_check_paths = { - 'files': ['bin/llvm-ar'], + 'files': ['bin/llvm-ar', 'bin/FileCheck'], 'dirs': ['include/llvm', 'include/llvm-c'], } -- GitLab From f8842a7e96418b884e6dbdbfa0eb6d8f59dc7981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 20:12:42 +0200 Subject: [PATCH 0538/2403] add easyconfig Rust-1.8.0-intel-2016a.eb --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb new file mode 100644 index 0000000000..e2f00427e8 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +dependencies = [ + ('LLVM', '3.8.0'), +] + +configopts = "--llvm-root=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From eaef4d4ce138181088a256bc62175b61bda94114 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2016 22:05:31 +0200 Subject: [PATCH 0539/2403] add easyconfig HDF-4.2.11-intel-2016a.eb --- .../h/HDF/HDF-4.2.11-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb new file mode 100644 index 0000000000..1d7ce9b8e5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.11' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From b0b683b2d704da4733dd791e2041277c6be48968 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 19 Apr 2016 23:31:46 -0400 Subject: [PATCH 0540/2403] add libQGLViewer easyconfig for foss 2016a --- .../libQGLViewer-2.6.3-foss-2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..12e821c14c --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -0,0 +1,18 @@ +easyblock = 'EB_libQGLViewer' + +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' + +moduleclass = 'lib' -- GitLab From 2a6a0dcb8c30c4edc6ac385c528b424601686ee1 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 01:15:13 -0400 Subject: [PATCH 0541/2403] add GDB 7.10.1 easyconfig for foss 2016a --- .../GDB-7.10.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7a28658458 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.10.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-python' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From e331243065a34afc93b9af7cc0603fc8faff5b89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 09:30:40 +0200 Subject: [PATCH 0542/2403] modify easyconfig HDF-4.2.11-intel-2016a.eb --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 1d7ce9b8e5..28e5e6ad36 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ ('Szip', '2.1'), + ('libjpeg-turbo', '1.4.2'), ] configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" -- GitLab From 62cc9b3e75ad621c2b74b36f8d6afe3c373c39d9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:16:16 +0200 Subject: [PATCH 0543/2403] Adjusted MADlib to supported postgresql version --- .../MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb index 35ae5d23c5..074b5142d7 100644 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb @@ -12,18 +12,25 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] -builddependencies = [('CMake', '3.4.3')] +builddependencies = [ + ('CMake', '3.4.3'), + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('M4', '1.4.17'), + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('PyXB', '1.2.4', versionsuffix), +] dependencies = [ ('Python', '2.7.11'), - ('PostgreSQL', '9.5.2', versionsuffix), + ('PostgreSQL', '9.4.7', versionsuffix), ] separate_build_dir = True sanity_check_paths = { 'files': ['bin/madpack'], - 'dirs': [] } moduleclass = 'data' -- GitLab From 5ad7cefb45a8dc6d5129d7196242ccd18fd01f2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:47:49 +0200 Subject: [PATCH 0544/2403] Add Postgres-XL --- ...gres-XL-9.5r1-intel-2016a-Python-2.7.11.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..01c5da8a48 --- /dev/null +++ b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Postgres-XL' +version = '9.5r1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.postgres-xl.org' +description = """Postgres-XL is a horizontally scalable open source SQL database cluster, +flexible enough to handle varying database workloads:""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://files.postgres-xl.org'] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' -- GitLab From ef50f1d4407173b2965c5a94a07d89f9a83fdb40 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:48:32 +0200 Subject: [PATCH 0545/2403] Add PostgreSQL 9.4.7 (needed for compatibility of MADlib) --- ...tgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..20f36a2447 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.22.1'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From fa95df64e5dc0ca93d6df41a3c32f7d125be6d22 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 10:52:01 +0200 Subject: [PATCH 0546/2403] Drop MADlib in this PR --- .../MADlib-1.9-intel-2016a-Python-2.7.11.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb deleted file mode 100644 index 074b5142d7..0000000000 --- a/easybuild/easyconfigs/m/MADlib/MADlib-1.9-intel-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MADlib' -version = '1.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://madlib.incubator.apache.org' -description = """MADlib: Big Data Machine Learning in SQL for Data Scientists""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -sources = ['apache-madlib-%(version)s-incubating-source.tar.gz'] -source_urls = ['https://dist.apache.org/repos/dist/release/incubator/madlib/%(version)s-incubating'] - -builddependencies = [ - ('CMake', '3.4.3'), - ('Bison', '3.0.4'), - ('flex', '2.6.0'), - ('M4', '1.4.17'), - ('Boost', '1.60.0', versionsuffix), - ('Eigen', '3.2.7'), - ('PyXB', '1.2.4', versionsuffix), -] - -dependencies = [ - ('Python', '2.7.11'), - ('PostgreSQL', '9.4.7', versionsuffix), -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['bin/madpack'], -} - -moduleclass = 'data' -- GitLab From 677926d3c95857f05067e4b2c6fc06088948ef07 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 11:02:33 +0200 Subject: [PATCH 0547/2403] Extend sanity check postgreSQL --- .../PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 4 ++-- .../PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index 20f36a2447..9afa456cae 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index a7590c6580..fca7dea11c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -37,8 +37,8 @@ builddependencies = [ configopts = '--with-python --with-openssl' sanity_check_paths = { - 'files': ['bin/psql'], - 'dirs': [], + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], } moduleclass = 'data' -- GitLab From 40dfcc220736688ada38def26b300fd15ae280ed Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 17:46:24 +0800 Subject: [PATCH 0548/2403] use patch to disable including arck.mk and define everything in prebuildopts --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 19 +++++++--- ...keleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 35 +++++++++++++++++++ .../BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 +++++++ 3 files changed, 62 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 6b0669dd87..7b6ed07c7d 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -4,8 +4,8 @@ name = 'BerkeleyGW' version = "1.0.6" homepage = 'http://www.berkeleygw.org' -description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} @@ -15,10 +15,21 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] +patches = ['BerkeleyGW_ignore_archmk.patch'] + files_to_copy = ['*'] -prebuildopts = 'touch arch.mk; ' +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts = 'all-flavors' -parallel = 1 +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..2001776308 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'BerkeleyGW' +version = "1.1-beta2" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk + periodic crystals to nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] + +patches = ['BerkeleyGW_ignore_archmk.patch'] + +files_to_copy = ['*'] + +prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' +prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' +prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' +prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' + +buildopts = 'all-flavors' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch new file mode 100644 index 0000000000..47898699a6 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch @@ -0,0 +1,12 @@ +avoid including arch.mk, which contains hardcoding settings we don't need/want +author: Miguel Dias Costa (National University of Singapore) +--- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 ++++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 +@@ -1,5 +1,5 @@ +-$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) +-include $(PREFIX)/arch.mk ++#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) ++#include $(PREFIX)/arch.mk + + ifneq ($(wildcard $(PREFIX)/flavor.mk),) + include $(PREFIX)/flavor.mk -- GitLab From cb89189505ade779e2cd9cb9da9bb29f254db6fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:23:46 +0200 Subject: [PATCH 0549/2403] ALPS now builds! --- .../ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 8 ++++---- .../a/ALPS/ALPS-2.2.b4-python-embedding.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index cf98c0aae4..ce0520f4ab 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://alps.comp-phys.org/static/software/releases'] +patches = ['ALPS-%(version)s-python-embedding.patch'] + builddependencies = [('CMake', '3.4.3')] dependencies = [ @@ -29,11 +31,9 @@ configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -maxparallel = 1 - sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/alpspython', 'lib/libalps.%s' % SHLIB_EXT], + 'dirs': ['include/alps', 'lib/python'] } moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch new file mode 100644 index 0000000000..5927e2e784 --- /dev/null +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-python-embedding.patch @@ -0,0 +1,14 @@ +# To embed python, it must return a list of needed libraries with `;` instead of whitespace +# Ward Poelmans +diff -ur alps-2.2.b4-src.orig/alps/config/FindPython.cmake alps-2.2.b4-src/alps/config/FindPython.cmake +--- alps-2.2.b4-src.orig/alps/config/FindPython.cmake 2015-09-20 21:21:42.000000000 +0200 ++++ alps-2.2.b4-src/alps/config/FindPython.cmake 2016-04-20 11:28:18.828407677 +0200 +@@ -160,7 +160,7 @@ + # + # libraries which must be linked in when embedding + # +- EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip()" ++ EXEC_PYTHON_SCRIPT ("from distutils.sysconfig import * ;print (str(get_config_var('LOCALMODLIBS')) + ' ' + str(get_config_var('LIBS'))).strip().replace(' ', ';')" + PYTHON_EXTRA_LIBS) + MESSAGE(STATUS "PYTHON_EXTRA_LIBS =${PYTHON_EXTRA_LIBS}" ) + mark_as_advanced(PYTHON_EXTRA_LIBS) -- GitLab From 523b4f05f0dc5b78abb1323e9ddf4cdbab5a86ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Apr 2016 13:26:34 +0200 Subject: [PATCH 0550/2403] add easyconfig Rust-1.8.0-foss-2016a.eb --- .../r/Rust/Rust-1.8.0-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb new file mode 100644 index 0000000000..2254e51fbf --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.8.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 240bbc87f7f4d346cedc3b29e326d7103fc24898 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:35:52 +0200 Subject: [PATCH 0551/2403] Let ALPS find Szip --- .../a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb index ce0520f4ab..74ee42be3a 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.2.b4-intel-2016a-Python-2.7.11.eb @@ -20,14 +20,14 @@ builddependencies = [('CMake', '3.4.3')] dependencies = [ ('zlib', '1.2.8'), + ('Szip', '2.1'), ('Python', '2.7.11'), ('Boost', '1.58.0', versionsuffix), ('HDF5', '1.8.16'), ('matplotlib', '1.5.1', versionsuffix), ] -configopts = '-DSZIP_INCLUDE_DIR=$EBROOTSZIP/include -DSZIP_LIBRARY=$EBROOTSZIP/lib ' -configopts += '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' +configopts = '-DFFTW_LIBRARIES=$FFTW_LIB_DIR -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR' separate_build_dir = True -- GitLab From 11b5379ba4bf016e2b2346f903746b7fd7f76a2f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 13:52:50 +0200 Subject: [PATCH 0552/2403] Fix remarks --- ...ntel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-7.11-intel-2016a.eb => GDB-7.11-intel-2016a-Python-2.7.11.eb} (95%) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb similarity index 95% rename from easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb rename to easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb index fa5295e98e..7f2305c130 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-intel-2016a-Python-2.7.11.eb @@ -2,14 +2,17 @@ easyblock = 'ConfigureMake' name = 'GDB' version = '7.11' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" +toolchain = {'name': 'intel', 'version': '2016a'} + sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'intel', 'version': '2016a'} +patches = ['GDB-7.9-missing-makeinfo.patch'] dependencies = [ ('zlib', '1.2.8'), @@ -19,8 +22,6 @@ dependencies = [ ('Python', '2.7.11'), ] -patches = ['GDB-7.9-missing-makeinfo.patch'] - configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' configopts += '--with-system-readline --enable-tui --enable-plugins' -- GitLab From 2f64f6c34e127ecd2095843c44409d7690926f31 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 14:52:09 +0200 Subject: [PATCH 0553/2403] Add explicit include for fslsurface --- easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index 145ff09b91..a26ad87936 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -14,6 +14,8 @@ patches = [ 'FSL_icc_nan-inf_fix.patch', ] +preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' + dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), -- GitLab From 3993ccc5f2970b1a36159c23a3681e14c025a912 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:00:08 +0200 Subject: [PATCH 0554/2403] Fix Werror error for MariaDB --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 8 ++++++-- .../m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 68f736cb1a..9a05f86ff3 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,19 +11,23 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-%(version)s-remove-Werror.patch'] + dependencies = [ ('zlib', '1.2.8'), ('ncurses', '6.0'), ('jemalloc', '4.1.0'), ('PCRE', '8.38'), ('XZ', '5.2.2'), - ('Boost', '1.60.0'), + ('Boost', '1.60.0', '-Python-2.7.11'), ('libxml2', '2.9.3'), ] builddependencies = [('CMake', '3.4.3')] -configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DWITH_INNODB_LZMA=on" +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON" sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch new file mode 100644 index 0000000000..c7d04caf71 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -0,0 +1,14 @@ +diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake +--- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 ++++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 +@@ -156,8 +156,8 @@ + endif () + + ## always want these +-set(CMAKE_C_FLAGS "-Wall -Werror ${CMAKE_C_FLAGS}") +-set(CMAKE_CXX_FLAGS "-Wall -Werror ${CMAKE_CXX_FLAGS}") ++set(CMAKE_C_FLAGS "-Wall ${CMAKE_C_FLAGS}") ++set(CMAKE_CXX_FLAGS "-Wall ${CMAKE_CXX_FLAGS}") + + ## need to set -stdlib=libc++ to get real c++11 support on darwin + if (APPLE) -- GitLab From 7cf6555d3c10191f880df6b26dc146d344d44093 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 15:03:08 +0200 Subject: [PATCH 0555/2403] Add doc in patch for Mariadb --- .../easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch index c7d04caf71..eb1812a0ff 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-remove-Werror.patch @@ -1,3 +1,5 @@ +# This -Werror will cause the build to fail because of a warning about using the intel compiler +# Ward Poelmans diff -ur mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake --- mariadb-10.1.13.orig/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-03-24 10:12:12.000000000 +0100 +++ mariadb-10.1.13/storage/tokudb/PerconaFT/cmake_modules/TokuSetupCompiler.cmake 2016-04-20 14:29:31.019940551 +0200 -- GitLab From 7329ac036396459a8d987ba66b18919854db545a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:51:03 +0800 Subject: [PATCH 0556/2403] use env --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 7b6ed07c7d..573492b3f2 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2001776308..509645960b 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ patches = ['BerkeleyGW_ignore_archmk.patch'] files_to_copy = ['*'] -prebuildopts = 'COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' +prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -- GitLab From 730ffa4793fdb863db56e34ddd1624b256e014de Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 21:52:12 +0800 Subject: [PATCH 0557/2403] use short indent in description --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 573492b3f2..cf8c1e41cf 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.0.6" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 509645960b..2b7d7dc5ed 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -5,8 +5,8 @@ version = "1.1-beta2" homepage = 'http://www.berkeleygw.org' description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle - properties and the optical responses of a large variety of materials from bulk - periodic crystals to nanostructures such as slabs, wires and molecules.""" + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -- GitLab From 57cea100f5dbffb25d4f5eab4e15303622ab55a7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 16:23:37 +0200 Subject: [PATCH 0558/2403] Mariadb: link to -lrt --- .../m/MariaDB/MariaDB-10.1.13-intel-2016a.eb | 5 ++++- .../MariaDB-10.1.13-link-rt-for-jemalloc.patch | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index 9a05f86ff3..ae90e1a3ed 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] sources = [SOURCELOWER_TAR_GZ] -patches = ['MariaDB-%(version)s-remove-Werror.patch'] +patches = [ + 'MariaDB-%(version)s-remove-Werror.patch', + 'MariaDB-%(version)s-link-rt-for-jemalloc.patch', +] dependencies = [ ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch new file mode 100644 index 0000000000..780c41af5b --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -0,0 +1,14 @@ +# On older systems (like RHEL 6), jemalloc must also link to -lrt for getclock +# On RHEL 7 and greater, this is not needed as it's part of libc there. +# Ward Poelmans +diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemalloc.cmake +--- mariadb-10.1.13.orig/cmake/jemalloc.cmake 2016-03-24 10:12:10.000000000 +0100 ++++ mariadb-10.1.13/cmake/jemalloc.cmake 2016-04-20 16:21:18.102681504 +0200 +@@ -21,6 +21,7 @@ + SET(what bundled) + ELSE() + SET(libname jemalloc c) ++ SET(CMAKE_REQUIRED_LIBRARIES r) + SET(what system) + ENDIF() + -- GitLab From 6a3bab838e81554fef00f818ee20c01190c71f50 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 22:27:47 +0800 Subject: [PATCH 0559/2403] use ConfigureMake skipping configure instead of MakeCp --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index cf8c1e41cf..570e1b3636 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.0.6" @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 2b7d7dc5ed..4c7949cc07 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'BerkeleyGW' version = "1.1-beta2" @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] patches = ['BerkeleyGW_ignore_archmk.patch'] -files_to_copy = ['*'] +skipsteps = ['configure'] prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' @@ -27,6 +27,8 @@ prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLA buildopts = 'all-flavors' +installopts = 'INSTDIR=%(installdir)s' + sanity_check_paths = { 'files': [], 'dirs': ['bin'] -- GitLab From f3cb8d07b5b4c94abec4f892c8041313ee7f569f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Apr 2016 17:00:41 +0200 Subject: [PATCH 0560/2403] Typo fix --- .../m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch index 780c41af5b..c0a2cfee18 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-link-rt-for-jemalloc.patch @@ -8,7 +8,7 @@ diff -ur mariadb-10.1.13.orig/cmake/jemalloc.cmake mariadb-10.1.13/cmake/jemallo SET(what bundled) ELSE() SET(libname jemalloc c) -+ SET(CMAKE_REQUIRED_LIBRARIES r) ++ SET(CMAKE_REQUIRED_LIBRARIES rt) SET(what system) ENDIF() -- GitLab From 8bce4c48707f8a6e4cc85986c6e013b1085c99a4 Mon Sep 17 00:00:00 2001 From: jgp Date: Wed, 20 Apr 2016 10:05:19 -0500 Subject: [PATCH 0561/2403] PrgEnv-pgi should not be version pinned --- easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 5de532fe82..112a9312bc 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -10,11 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version - # ('PrgEnv-pgi/' + version, EXTERNAL_MODULE), - ('PrgEnv-pgi/5.2.82', EXTERNAL_MODULE), + ('PrgEnv-pgi', EXTERNAL_MODULE), ('pgi/16.3.0' , EXTERNAL_MODULE), ('cray-mpich/7.3.2', EXTERNAL_MODULE), - # ('cray-libsci/16.03.1', EXTERNAL_MODULE), # Cray does not provide cray-libsci for PrgEnv-pgi ] moduleclass = 'toolchain' -- GitLab From ee8043a440abb6accfb24a556ccdb1e391f8c3e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Apr 2016 23:19:34 +0800 Subject: [PATCH 0562/2403] add most important binaries to sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 6 ++++-- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 570e1b3636..2b338d6458 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4c7949cc07..42d4b94976 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,10 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] + 'files': ['bin/'+name+'.'+flavor+'.x' + for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + for flavor in ['real', 'cplx']], + 'dirs': [] } moduleclass = 'chem' -- GitLab From 062b8f678410ec70835f69b578bf2778f8f4346a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 00:04:37 +0800 Subject: [PATCH 0563/2403] don't redefine variable 'name' in sanity_check_path --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 4 ++-- .../BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 2b338d6458..452f967939 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 42d4b94976..04a46cfa50 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -30,8 +30,8 @@ buildopts = 'all-flavors' installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+name+'.'+flavor+'.x' - for name in ['epsilon', 'sigma', 'kernel', 'absorption'] + 'files': ['bin/'+prog+'.'+flavor+'.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] } -- GitLab From 40d739240753148a555a9d0432149f88d93a293d Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 20 Apr 2016 16:47:30 -0400 Subject: [PATCH 0564/2403] including libGLU 9.0.0 as dependency --- .../l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index 12e821c14c..cd9274f066 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -11,8 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.libqglviewer.com/src/'] sources = [SOURCE_TAR_GZ] +dependencies = [ + ('libGLU', '9.0.0'), +] + builddependencies = [('Qt', '4.8.7')] -start_dir = '%(builddir)s/libQGLViewer-2.6.3/QGLViewer' +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' moduleclass = 'lib' -- GitLab From d85d97170461ddf8f1b654addca47fc8dfcd2897 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:57:05 +0800 Subject: [PATCH 0565/2403] remove patch, copy generic arch.mk instead --- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 14 ++++++-------- .../b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch | 12 ------------ 3 files changed, 12 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 452f967939..ef88631251 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['8740562da41e87a62eb8d457675e4bfd'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 04a46cfa50..07d5635dac 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -15,17 +15,15 @@ source_urls = ['http://www.berkeleygw.org/releases/'] sources = ['BGW-%(version)s.tar.gz'] checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] -patches = ['BerkeleyGW_ignore_archmk.patch'] - skipsteps = ['configure'] -prebuildopts = 'env COMPFLAG=-DINTEL PARAFLAG=-DMPI MATHFLAG=-DUSESCALAPACK FCPP="cpp -ansi" F90free="$MPIF90 -free" ' -prebuildopts += 'LINK="$MPIF90" FOPTS="$FFLAGS" MOD_OPT="-module " INCFLAG="-I" C_PARAFLAG=-DPARA CC_COMP="$MPICXX" ' -prebuildopts += 'C_COMP="$MPICC" C_LINK="$MPICXX" C_OPTS="$CFLAGS" REMOVE="/bin/rm -f" MKLPATH="$MKLROOT" ' -prebuildopts += 'FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" FFTWINCLUDE="$FFTW_INC_DIR" ' -prebuildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' -buildopts = 'all-flavors' +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' installopts = 'INSTDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch deleted file mode 100644 index 47898699a6..0000000000 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW_ignore_archmk.patch +++ /dev/null @@ -1,12 +0,0 @@ -avoid including arch.mk, which contains hardcoding settings we don't need/want -author: Miguel Dias Costa (National University of Singapore) ---- Common/common-rules.mk.orig 2016-04-20 13:44:00.254262000 +0800 -+++ Common/common-rules.mk 2016-04-20 13:44:07.830742486 +0800 -@@ -1,5 +1,5 @@ --$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) --include $(PREFIX)/arch.mk -+#$(if $(wildcard $(PREFIX)/arch.mk),,$(error Error: Please create arch.mk from config/ directory for machine-dependent configuration)) -+#include $(PREFIX)/arch.mk - - ifneq ($(wildcard $(PREFIX)/flavor.mk),) - include $(PREFIX)/flavor.mk -- GitLab From d62ec8db0c825e6d49318e8b7ca39ae771e67717 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 21 Apr 2016 15:58:49 +0800 Subject: [PATCH 0566/2403] edit homepage --- .../a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index ca4b5697db..a8183634de 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.10.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'ASE' version = '3.10.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://wiki.fysik.dtu.dk/ase/' +homepage = 'http://wiki.fysik.dtu.dk/ase' description = """ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.""" -- GitLab From 6c33d10734fc28919e332f46e9379110bcd0a316 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 Apr 2016 10:50:17 +0200 Subject: [PATCH 0567/2403] Fix remarks --- .../easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb index e13485c431..7bee41cdcd 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.1.0-intel-2016a.eb @@ -19,10 +19,10 @@ prebuildopts = "make dist && " sanity_check_paths = { 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, - 'lib/libjemalloc.so.2', 'include/jemalloc/jemalloc.h'], + 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } -modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.2']} +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' -- GitLab From 4cf2eea4df6c8009160944677838d710c796c45d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:26:15 +0200 Subject: [PATCH 0568/2403] Updated easyconfig for Extrae --- .../e/Extrae/Extrae-3.0.1-foss-2015a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb new file mode 100644 index 0000000000..52f70c46db --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Extrae" +version = "3.0.1" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +compname = 'GCC' +compver = '4.8.3' + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22', "", (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), + ('libunwind', '1.1', "", (compname, compver)), + ('libxml2', '2.9.2', "", (compname, compver)), + ('libdwarf', '20150310', "", (compname, compver)), + ('PAPI', '5.4.1'), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +moduleclass = 'perf' -- GitLab From fe659cbc50239dfb0b128bca3a87430c52976f79 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:35:43 +0200 Subject: [PATCH 0569/2403] Add easyconfigs for dependencies --- .../b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb | 25 ++++++++++ .../l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb | 35 ++++++++++++++ .../l/libelf/libelf-0.8.13-GCC-4.8.3.eb | 19 ++++++++ .../l/libunwind/libunwind-1.1-GCC-4.8.3.eb | 23 ++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb | 23 ++++++++++ .../p/PAPI/PAPI-5.4.1-foss-2015a.eb | 46 +++++++++++++++++++ 6 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb new file mode 100644 index 0000000000..1284a2ff8d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.8.3-serial.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source +libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +toolset = 'gcc' + +osdependencies = [('zlib-devel','zlib1g-dev')] + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb new file mode 100644 index 0000000000..251774788a --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.8.3.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'libdwarf' +version = '20140805' + +homepage = 'http://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.prevanders.net'] + +dependencies = [('libelf', '0.8.13')] + +with_configure = True +preconfigopts = 'CFLAGS="-fPIC $CFLAGS" ' +configopts = "--enable-shared " + +# This is dirty but libdwarf cannot find it's own library in the build process... +prebuildopts = ' LD_LIBRARY_PATH="../libdwarf:$LD_LIBRARY_PATH" ' + +files_to_copy = [ + (["dwarfdump2/dwarfdump"], "bin"), + (["libdwarf/libdwarf.a", "libdwarf/libdwarf.so"], "lib"), + (["libdwarf/libdwarf.h", "libdwarf/dwarf.h"], "include"), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin", "lib", "include"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb new file mode 100644 index 0000000000..5a843a2867 --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'http://www.mr511.de/software/english.html' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.mr511.de/software/'] + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.so', 'lib/libelf.so.0', 'include/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb new file mode 100644 index 0000000000..fb68bfa6c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = "libunwind" +version = "1.1" + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib64/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000..36ce015707 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +#dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb new file mode 100644 index 0000000000..b5babf4529 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.1' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 4afabab6c7531707ac95380064ee8104f82f970c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 21 Apr 2016 11:43:09 +0200 Subject: [PATCH 0570/2403] Updated easyconfigs for Paraver and dependencies --- .../p/Paraver/Paraver-4.5.6-foss-2015a.eb | 33 +++++++++++++++++++ .../wxPropertyGrid-1.4.15-GCC-4.8.3.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb create mode 100644 easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb new file mode 100644 index 0000000000..03007f6aa9 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Paraver" +version = "4.5.6" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +compname = 'GCC' +compver = '4.8.3' + +dependencies = [ + ('wxPropertyGrid', '1.4.15', "", (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), +] + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb new file mode 100644 index 0000000000..3c8c6c406c --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.8.3.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = "wxPropertyGrid" +version = "1.4.15" + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +osdependencies = ['wxWidgets-ansi-devel'] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ["include/wx/propgrid/propgrid.h", "lib64/libwxcode_gtk2_propgrid-2.8.so"], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' -- GitLab From 6a4d11c588f7e31daf36f0f34262d769f3c1f92f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 08:41:23 +0800 Subject: [PATCH 0571/2403] generated with 'eb netCDF-Fortran-4.4.2-intel-2015b.eb --try-toolchain=intel,2016.02-GCC-4.9 -r' --- .../Bison-3.0.4-intel-2016.02-GCC-4.9.eb | 22 ++++++++++++ .../CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++ .../Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb | 19 +++++++++++ .../flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb | 14 ++++++++ ...DF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb | 26 ++++++++++++++ .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ++++++++++ ...CDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb | 20 +++++++++++ .../netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 34 +++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb | 23 +++++++++++++ 10 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..64d95d529f --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..c09f6ccec0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..7135e0d493 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.45.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..6c27df0850 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.10-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.10' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.4.1'), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..154963c1c8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..42dda90335 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..5385893f9b --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,18 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 +buildopts = 'CPP="$CC -E -P"' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..80d70623d7 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..a58bf39670 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.15-patch1'), + ('cURL', '7.45.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..d8f05c9dd2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c87e72f236cf524b40675127c28af5e3e637a479 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:14:39 -0400 Subject: [PATCH 0572/2403] include Loki as dependency of Yade --- .../l/Loki/Loki-0.1.7-foss-2016a.eb | 23 +++++++++++++++++++ .../l/Loki/Loki-0.1.7_change_prefix.patch | 9 ++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb new file mode 100644 index 0000000000..dcb7370cfb --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +preinstallopts = "export EB_INSTALL_DIR=%(installdir)s &&" + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +patches = [('Loki-0.1.7_change_prefix.patch')] diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch new file mode 100644 index 0000000000..8a0666c803 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch @@ -0,0 +1,9 @@ +diff -ru loki-0.1.7.orig/Makefile.common loki-0.1.7/Makefile.common +--- loki-0.1.7.orig/Makefile.common 2007-05-28 22:26:26.000000000 -0400 ++++ loki-0.1.7/Makefile.common 2016-04-21 18:20:54.280476472 -0400 +@@ -4,4 +4,4 @@ + CXXWARNFLAGS := -Wall -Wold-style-cast -Wundef -Wsign-compare -Wconversion -Wpointer-arith -pedantic + CXXFLAGS := $(CXXWARNFLAGS) -g -O2 + +-prefix := /usr ++prefix := $(EB_INSTALL_DIR) -- GitLab From b19ad0a671fe667e1e66833ee29de83515a95e62 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:28:24 -0400 Subject: [PATCH 0573/2403] add minieigen easyconfig --- .../Boost-1.60.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++ .../m/minieigen/minieigen-0.5.3-foss-2016a.eb | 28 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a913c20849 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb new file mode 100644 index 0000000000..9012d7f022 --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('Python', '2.7.11'), +] + +#incomplete +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'lib' -- GitLab From f14b5d592e7c8f9f679adc07e1acd3946fff8c27 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 02:31:24 -0400 Subject: [PATCH 0574/2403] improve Yade easyconfig but still not finished --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 66 ++++++++----------- 1 file changed, 28 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb index 3711be5fc1..83be6ba55d 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'Yade' version = '1.20.0' -homepage = 'www.yade-dem.org' +homepage = 'https://yade-dem.org/doc/' description = """ Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. @@ -14,50 +14,38 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('git', '2.8.0'), - ('freeglut', '3.0.0'), - ('loki', '-------'), - ('Boost', '1.60.0'), - ('fakeroot', '-------'), - ('dpkg', '-------'), - ('IPython', '3.2.3', versionsuffix), - ('matplotlib', '1.5.1'), - ('SQLite', '3.9.2'), - ('numpy', '1.10.4', versionsuffix) - ('TK', '8.6.4', 'no-X11'), - ('gnuplot', '5.0.3'), - ('gts', '0.7.6'), - ('Graphviz', '2.38'), - ('ScientificPython', '2.9.4', versionsuffix), + ('Loki', '0.1.7'), + ('Boost', '1.60.0', versionsuffix), +# ('IPython', '3.2.3', versionsuffix), +# ('matplotlib', '1.5.1'), +# ('SQLite', '3.9.2'), + ('numpy', '1.8.2', versionsuffix), ('Eigen', '3.2.7'), - ('Qt', '4.8.7'), - ('gtk+', '2.24.28'), - ('libqglviewer-dev', '-------'), - ('libjs-jquery', '---------'), - ('Sphinx', '1.3.3'), - ('bibtexparser', '0.6.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6'), - ('help2man', '--------'), - ('bzip2', '1.0.6'), - ('ziblg-dev', '---------------'), - ('GDB', '7.10.1',versionsuffix), + ('minieigen', '0.5.3') + ('Qt', '4.8.7'), + ('Python', '2.7.11'), +# ('libQGLViewer', '2.6.3'), +# ('GDB', '7.10.1',versionsuffix), # optional - ('VTK', '6.3.0'), - ('CGAL', '4.7'), - ('SuiteSparse', '4.5.1'), - ('OpenBLAS', '0.2.15'), - ('METIS', '5.1.0'), +# ('VTK', '6.3.0'), +# ('CGAL', '4.7'), +# ('SuiteSparse', '4.5.1'), +# ('OpenBLAS', '0.2.15'), +# ('METIS', '5.1.0'), ] -builddependencies = [('CMake', '3.2.3')] +builddependencies = [('CMake', '3.4.3')] separate_build_dir = True +configopts = '-DENABLE_GUI=OFF' +configopts += '-DENABLE_VTK=OFF' +configopts += '-DENABLE_CGAL=OFF' +configopts += '-DENABLE_PFVFLOW=OFF' + # In case you want disable some Yade features # configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' @@ -80,9 +68,11 @@ separate_build_dir = True # VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) # USE_QT5: use QT5 for GUI, experimental (OFF by default) + +#incomplete sanity_check_paths = { - 'files': ['bin/%s-%s' %(namelower, version), 'bin/%s-%s-batch' %(namelower, version)], - 'dirs': ['lib/x86_64-linux-gnu'] + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch'], + 'dirs': ["."] } moduleclass = 'devel' -- GitLab From af63af4269d95dc953f708bbaf55655f30273915 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:17:53 +0800 Subject: [PATCH 0575/2403] [phys]{intel/2016.02-GCC-4.9} Yambo 3.4.2 --- .../Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..aaa16d016b --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Yambo' +version = '3.4.2' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +dependencies = [('netCDF-Fortran', '4.4.2')] + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +checksums = ['f0820a0f42dfc81ce3811af647bed777'] + +configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' + +buildopts = 'all' + +# no make install +buildininstalldir = 'True' +skipsteps = ['install'] +modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], + 'dirs': [] +} + +moduleclass = 'phys' + +parallel = 1 -- GitLab From 2eca14f6b542eb457c27f4aebe36d6fb4496f7ee Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:30:48 +0800 Subject: [PATCH 0576/2403] bump ncurses to 6.0 --- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index c09f6ccec0..df5823de42 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1p'), -- GitLab From b76df745227c017890c908f28810ae55c805ae1b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 15:42:27 +0800 Subject: [PATCH 0577/2403] change module class --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index ef88631251..c0d639cc89 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 07d5635dac..4700de27c4 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -34,4 +34,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'chem' +moduleclass = 'phys' -- GitLab From 22fc709acd211c30baf89829b9cafdaa0709e873 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 16:54:42 +0800 Subject: [PATCH 0578/2403] remove ncurses-5.9-intel-2016.02-GCC-4.9.eb --- .../ncurses-5.9-intel-2016.02-GCC-4.9.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb deleted file mode 100644 index 5385893f9b..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2016.02-GCC-4.9.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'ncurses' -version = '5.9' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 -buildopts = 'CPP="$CC -E -P"' - -moduleclass = 'devel' -- GitLab From e20edb315e0af6f790c4efa27e69eb4f887bd960 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:29:16 +0800 Subject: [PATCH 0579/2403] bump HDF5 to 1.8.16 and cURL to 7.47.0 --- ...016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} | 4 ++-- ...016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} | 2 +- .../n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/cURL/{cURL-7.45.0-intel-2016.02-GCC-4.9.eb => cURL-7.47.0-intel-2016.02-GCC-4.9.eb} (94%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb => HDF5-1.8.16-intel-2016.02-GCC-4.9.eb} (96%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb similarity index 94% rename from easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb index 7135e0d493..45e6650292 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.45.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.47.0-intel-2016.02-GCC-4.9.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'cURL' -version = '7.45.0' +version = '7.47.0' homepage = 'http://curl.haxx.se' description = """libcurl is a free and easy-to-use client-side URL transfer library, @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -# dependencies = [('OpenSSL', '1.0.1p')] +# dependencies = [('OpenSSL', '1.0.1s')] # configopts = "--with-ssl=$EBROOTOPENSSL" modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb similarity index 96% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb index 42dda90335..d1c17ce30e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,5 @@ name = 'HDF5' -version = '1.8.15-patch1' +version = '1.8.16' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb index a58bf39670..cff46757ad 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -16,8 +16,8 @@ source_urls = [ ] dependencies = [ - ('HDF5', '1.8.15-patch1'), - ('cURL', '7.45.0'), + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), ] builddependencies = [ -- GitLab From bc66427075d6045dce28ff41b2364668b5b56436 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:37:27 +0800 Subject: [PATCH 0580/2403] fix source_urls --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index aaa16d016b..f1e84f6a06 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} dependencies = [('netCDF-Fortran', '4.4.2')] sources = [SOURCELOWER_TGZ] -source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/yambo-3.4.2.tgz'] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' -- GitLab From 6eca75d940ee822d1eab2eb2c88e973f3b4d596a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 17:38:22 +0800 Subject: [PATCH 0581/2403] move dependencies below checksums --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index f1e84f6a06..bcb6f56739 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -10,12 +10,12 @@ description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid s toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -dependencies = [('netCDF-Fortran', '4.4.2')] - sources = [SOURCELOWER_TGZ] source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] checksums = ['f0820a0f42dfc81ce3811af647bed777'] +dependencies = [('netCDF-Fortran', '4.4.2')] + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -- GitLab From 595721d4fb95078144d99129ff0a28a394b79ed2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:48:07 +0200 Subject: [PATCH 0582/2403] Biopython sanity check fix --- .../Biopython-1.65-foss-2016a-2.7.11.eb | 45 ------------------- ...Biopython-1.65-foss-2016a-Python-2.7.11.eb | 13 +++--- 2 files changed, 5 insertions(+), 53 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb deleted file mode 100644 index fc337c6c52..0000000000 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-2.7.11.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas -# License:: MIT/GPL -# -## -easyblock = "PythonPackage" - -name = 'Biopython' -version = '1.65' - -homepage = 'http://www.biopython.org' -description = """Biopython is a set of freely available tools for biological computation written -in Python by an international team of developers. It is a distributed collaborative effort to -develop Python libraries and applications which address the needs of current and future work in -bioinformatics. """ - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://biopython.org/DIST'] -sources = ['%(namelower)s-%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%s-%s" % (python, pyver) - -dependencies = [ - (python, pyver), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] -} - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 8730db898f..822334825f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -29,18 +29,15 @@ pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pyver), - ('numpy', '1.10.1', versionsuffix) + (python, pyver) ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, - 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\ - pyshortver), - 'lib/python%s/site-packages/BioSQL' % pyshortver] + 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 9bca295d623e5a844af78e774d8d2e8752b28006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 11:49:20 +0200 Subject: [PATCH 0583/2403] String fix --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 822334825f..f4b92dace0 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ python = 'Python' pyver = '2.7.11' pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = "-%s-%s" % (python, pyver) +versionsuffix = "-%(python)s-%(pyver)s" dependencies = [ (python, pyver) -- GitLab From 5e94418f4931181e31c47d3be9882d0e6f232dc8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:18:51 +0800 Subject: [PATCH 0584/2403] remove library paths, not needed --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index bcb6f56739..e98b1483ff 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -19,7 +19,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' -configopts += '--with-netcdf-libs="-L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff -L$EBROOTNETCDF/lib64 -lnetcdf"' +configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 37731eef8b1705bc86ad2224890ed318bc6e4329 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:33:13 +0800 Subject: [PATCH 0585/2403] use $LIBFFT --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index e98b1483ff..4f192a0588 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ dependencies = [('netCDF-Fortran', '4.4.2')] configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' -configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="-mkl" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -- GitLab From 98b99c783631409424f36993ac8b6a14de0f74ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:11 +0200 Subject: [PATCH 0586/2403] add easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- ...numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f3e0914bd5 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 4046ca8caf31526416dc2842edef61a8b2eb32b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:29 +0200 Subject: [PATCH 0587/2403] add easyconfig gdist-1.0.3-intel-2016a-Python-2.7.11.eb --- .../gdist-1.0.3-intel-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f6f38f5d9f --- /dev/null +++ b/easybuild/easyconfigs/g/gdist/gdist-1.0.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'gdist' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gdist' +description = """The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for + computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three + dimensions, such that the line lies on the surface.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 86b9fbf96e643400c35e6ce3eefa37323fe758a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 12:43:44 +0200 Subject: [PATCH 0588/2403] ext list ? --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index c3ca739024..1e9c0c19f5 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,6 +18,12 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), +] options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 5307a71e915dea2e5c22e0a634ffd5129298aac2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 12:43:52 +0200 Subject: [PATCH 0589/2403] add easyconfig NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb, add easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb, add easyconfig pydicom-0.9.9-intel-2016a-Python-2.7.11.eb --- ...NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb | 29 +++++++++++++++ .../PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ ...pydicom-0.9.9-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..77bcd52bff --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'NiBabel' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('PIL', '1.1.7', versionsuffix), + ('pydicom', '0.9.9', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f996585e10 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pyver), + ('libjpeg-turbo', '1.4.2'), + # currently not used because of dependency hell + # ('freetype', '2.6.1'), +] + +options = {'modulename': 'PIL'} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ab11ff4c9f --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-0.9.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '0.9.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/darcymason/pydicom' +description = """Read, modify and write DICOM files with python code""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/darcymason/pydicom/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +start_dir = 'source' + +options = {'modulename': 'dicom'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pydicom-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'data' -- GitLab From e2d71772432a501aed37e770db3eec9ea1ddcf08 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 18:58:14 +0800 Subject: [PATCH 0590/2403] switch to MakeCp with configure --- .../y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 4f192a0588..23778bb6d6 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'Yambo' version = '3.4.2' @@ -16,6 +16,8 @@ checksums = ['f0820a0f42dfc81ce3811af647bed777'] dependencies = [('netCDF-Fortran', '4.4.2')] +with_configure = 'True' + configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' configopts += '--with-scalapack-libs="$LIBSCALAPACK" --with-fft-libs="$LIBFFT" ' @@ -23,10 +25,7 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' -# no make install -buildininstalldir = 'True' -skipsteps = ['install'] -modextrapaths = {'PATH': '%(namelower)s-%(version)s/bin'} +files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', -- GitLab From d05d19be93bde3c4e31429ccaed73c50213b3406 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:43:38 +0200 Subject: [PATCH 0591/2403] modify easyconfig numexpr-2.5.2-intel-2016a-Python-2.7.11.eb --- .../n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb index f3e0914bd5..c352743328 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.5.2-intel-2016a-Python-2.7.11.eb @@ -11,7 +11,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 88ddd7a1b72945cb902ef2526ef8b8861b835be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 13:51:17 +0200 Subject: [PATCH 0592/2403] modify easyconfig PIL-1.1.7-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index f996585e10..dabb8b2f35 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -27,10 +27,9 @@ dependencies = [ options = {'modulename': 'PIL'} -pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib/python%s/site-packages/%%(name)s' % pyshortver], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], } moduleclass = 'vis' -- GitLab From 47f5dbe7cec4797ad7745b808c06525bbb6c5c14 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 22 Apr 2016 19:55:50 +0800 Subject: [PATCH 0593/2403] fix path in sanity checks --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 23778bb6d6..d06eb6d47f 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts = 'all' files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { - 'files': ['%(namelower)s-%(version)s/bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'files': ['bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], 'dirs': [] } -- GitLab From aa313b0431ca16e479e1be7c4795aa7befe6ad18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:34:28 +0200 Subject: [PATCH 0594/2403] usempi is not required for numexpr --- .../n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 1 - .../n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb | 1 - .../n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb index b59dd7b4f3..12e8271d88 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 0f25285835..986566870c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb index 585a1680b7..7b2e107b82 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb index a1e1df7d77..0012640a1c 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.4.6-intel-2015b-Python-2.7.10.eb @@ -10,7 +10,6 @@ description = """The numexpr package evaluates multiple-operator array expressio compiler at runtime.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'usempi': True} source_urls = ['https://github.com/pydata/numexpr/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From fbb287eb014e34d2f02e1f96ed017af399d46e51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 14:44:11 +0200 Subject: [PATCH 0595/2403] add easyconfig PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb new file mode 100644 index 0000000000..93ba3d3868 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(ppyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('libjpeg-turbo', '1.4.2'), + ('freetype', '2.6.3'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' -- GitLab From e2ced009d6dec638e457588563d90907b8a2f26f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 14:52:58 +0200 Subject: [PATCH 0596/2403] Commet with foss2016a --- ...ommet-20160422-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..037900565c --- /dev/null +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'Commet' +version = '20160422' + +homepage = 'https://colibread.inria.fr/software/commet/' +description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# there is no tarball provided, only git checkout through: +# https://github.com/pierrepeterlongo/commet/archive/master.zip +sources = [SOURCE_ZIP] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%(pythonversion)s' + +dependencies = [ + ('Python', pythonversion), +] + +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], + 'dirs' : ['doc','include'] +} + +moduleclass = 'bio' -- GitLab From 7ac6d46d9d2b1bf23b8bd44dd02adcd717c0b08f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 15:14:36 +0200 Subject: [PATCH 0597/2403] stick to freetype 2.6.2 for compatibility with matplotlib 1.5.1 --- .../p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb index dabb8b2f35..0fd64f3fd2 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'PIL' version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pythonware.com/products/pil' description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. @@ -15,14 +15,11 @@ sources = ['Imaging-%(version)s.tar.gz'] patches = ['PIL-%(version)s-find-deps.patch'] -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver dependencies = [ ('zlib', '1.2.8'), - ('Python', pyver), + ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), - # currently not used because of dependency hell - # ('freetype', '2.6.1'), + ('freetype', '2.6.2'), ] options = {'modulename': 'PIL'} -- GitLab From ab90ad2507bc8890a2aaa665e307cebe60f057d3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:29:11 +0200 Subject: [PATCH 0598/2403] fixed pyver --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 037900565c..abd2d674a6 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -3,6 +3,9 @@ easyblock = 'MakeCp' name = 'Commet' version = '20160422' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' + homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. """ @@ -14,11 +17,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_ZIP] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -pythonversion = '2.7.11' -versionsuffix = '-Python-%(pythonversion)s' dependencies = [ - ('Python', pythonversion), + ('Python', pyver), ] checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] @@ -28,4 +29,4 @@ sanity_check_paths = { 'dirs' : ['doc','include'] } -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From 3966bc3e025065c771252bae4528eee8d3c653e2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 22 Apr 2016 15:52:23 +0200 Subject: [PATCH 0599/2403] CrossTalkZ with foss 2016a --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb new file mode 100644 index 0000000000..f798c72eb5 --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From a9a96a44eecdb03cc1396f86fd35ad79e5a8c2db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 16:02:37 +0200 Subject: [PATCH 0600/2403] add test configuration for Travis --- .travis.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000000..07d8498dcd --- /dev/null +++ b/.travis.yml @@ -0,0 +1,18 @@ +language: python +python: + - 2.6 + - 2.7 +addons: + apt: + packages: + - tcl8.5 +install: + # install easybuild-framework/easybuild-easyblocks (and dependencies) + # use 'develop' branch of framework/easyblocks, except when testing 'master' + if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework + - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT +script: + - python -O -m test.easyconfigs.suite -- GitLab From e23363ce6f9b632096702d193242e5221c5f7cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 22 Apr 2016 16:06:42 +0200 Subject: [PATCH 0601/2403] Fix failing FSL on RHEL 7 --- .../easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb | 4 ++-- .../easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb index a26ad87936..5b9dfba11b 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2016a.eb @@ -11,15 +11,15 @@ sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', 'FSL_icc_nan-inf_fix.patch', ] -preconfigopts = 'CFLAGS="-I%(builddir)s/src $CFLAGS"' - dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.1.0'), ('libX11', '1.6.3'), + ('zlib', '1.2.8'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch new file mode 100644 index 0000000000..40e5baff2f --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9_missing_lib.patch @@ -0,0 +1,14 @@ +# On RHEL 7 and friends, you need to link to libglapi too +# Ward Poelmans +diff -ur fsl.oirg/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.oirg/src/fslsurface/Makefile 2014-02-24 12:09:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2016-04-21 18:03:50.246117983 +0200 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + -- GitLab From 54f93414557afa15e4d1234300f5a0ca53ff46d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:37:00 +0200 Subject: [PATCH 0603/2403] add easyconfig i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb --- ...-1.0-20160213-intel-2016a-Python-2.7.11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a0ac2c0885 --- /dev/null +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name ='i-PI' +version = '1.0-20160213' +commit = '2a09a6d' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/i-pi/i-pi' +description = """A Python wrapper for (ab initio) (path integrals) molecular dynamics""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/i-pi/i-pi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'ipi'} + +sanity_check_paths = { + 'files': ['bin/i-pi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From 48744e84a92f73b252f175f9925e0af41fc8f35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 17:46:56 +0200 Subject: [PATCH 0604/2403] make dev version PEP440 compliant --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 72cf85df21..cf1d254d29 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0dev0' +VERSION = '2.8.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 40f5979f3457df08f8f40f1afa54a122f9ad2ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 18:20:43 +0200 Subject: [PATCH 0605/2403] remove faulty PIL easyconfig --- ...PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb deleted file mode 100644 index 93ba3d3868..0000000000 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016a-Python-%(ppyver)s.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PIL' -version = '1.1.7' -versionsuffix = '-Python-%(ppyver)s' - -homepage = 'http://www.pythonware.com/products/pil' -description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. - This library supports many file formats, and provides powerful image processing and graphics capabilities.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['http://effbot.org/downloads/'] -sources = ['Imaging-%(version)s.tar.gz'] - -patches = ['PIL-%(version)s-find-deps.patch'] - -dependencies = [ - ('zlib', '1.2.8'), - ('Python', '2.7.11'), - ('libjpeg-turbo', '1.4.2'), - ('freetype', '2.6.3'), -] - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -moduleclass = 'vis' -- GitLab From 3209fcc10eff09c48149a435a4d568b3a8e7a94d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:06:07 +0200 Subject: [PATCH 0606/2403] query GitHub for commit ID of framework/easyblocks branch being used --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 07d8498dcd..de7edac95e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,9 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz + - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT -- GitLab From e2387d1953bd9797547e5da2016e2ec1bf333897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:12:42 +0200 Subject: [PATCH 0607/2403] fix typo --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index de7edac95e..9e395b922a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,7 +9,7 @@ addons: install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha -- GitLab From 643d94631fe876912443b51ad8eb7483da39c284 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:14:33 +0200 Subject: [PATCH 0608/2403] set $PYTHONPATH --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 9e395b922a..74257fabfb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,4 +17,5 @@ install: # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT script: + - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 9a7580590297de695981ebf84c327abb39fff3b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 19:48:22 +0200 Subject: [PATCH 0609/2403] install python-graph-core library required by easyconfig tests --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 74257fabfb..47842a3535 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,8 @@ addons: packages: - tcl8.5 install: + # required for test_dep_graph + - pip install python-graph-core # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From d65154ee61c23a8fdc6583d5a66920fb9aae445b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 20:03:14 +0200 Subject: [PATCH 0610/2403] also install python-graph-dot --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 47842a3535..a67e42aebf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,7 +8,7 @@ addons: - tcl8.5 install: # required for test_dep_graph - - pip install python-graph-core + - pip install python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From 7bce8c9d5f52d8d7a1588db7100f65e75adc16d5 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 22 Apr 2016 15:43:48 -0400 Subject: [PATCH 0611/2403] add patch to include Egien --- .../m/minieigen/minieigen-0.5.3-foss-2016a.eb | 2 ++ .../m/minieigen/minieigen-0.5.3_Eigen.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb index 9012d7f022..4a8f2d9f28 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] +patches = ['minieigen-0.5.3_Eigen.patch'] + versionsuffix = '-Python-%(pyver)s' dependencies = [ diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch new file mode 100644 index 0000000000..2d683420ff --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch @@ -0,0 +1,24 @@ +diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py +--- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 ++++ minieigen-0.5.3/setup.py 2016-04-22 15:34:16.527587398 -0400 +@@ -1,6 +1,6 @@ + # encoding: utf-8 + from distutils.core import setup,Extension +-import sys, glob ++import os, sys, glob + + # vectorization is currently broken and experimental ONLY + vectorize=False +@@ -19,10 +19,11 @@ + # * https://bugs.launchpad.net/panda3d/+bug/919237 + define_macros+=[('EIGEN_DONT_VECTORIZE',None)] + else: ++ eigen_prefix = os.environ["EBROOTEIGEN"] + py3k=(sys.version_info[0]==3) + libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] + library_dirs=[] +- include_dirs=['/usr/include/eigen3','/usr/local/include/eigen3','minieigen'] ++ include_dirs=['%s/include/eigen3' % eigen_prefix, 'minieigen'] + + setup(name='minieigen', + version='0.5.3', -- GitLab From e2b1e2bf1eea6eeee0813e05dd8a0e6d004c76f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2016 22:29:53 +0200 Subject: [PATCH 0612/2403] remove Rust easyconfig using intel toolchain, rustc doesn't work --- .../r/Rust/Rust-1.8.0-intel-2016a.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb deleted file mode 100644 index e2f00427e8..0000000000 --- a/easybuild/easyconfigs/r/Rust/Rust-1.8.0-intel-2016a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Rust' -version = '1.8.0' - -homepage = 'https://www.rust-lang.org' -description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, - and guarantees thread safety.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['https://static.rust-lang.org/dist/'] -sources = ['rustc-%(version)s-src.tar.gz'] - -builddependencies = [('Python', '2.7.11')] - -dependencies = [ - ('LLVM', '3.8.0'), -] - -configopts = "--llvm-root=$EBROOTLLVM" - -sanity_check_paths = { - 'files': ['bin/rustc', 'bin/rustdoc'], - 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], -} - -moduleclass = 'lang' -- GitLab From dea89b699b0c8bb51fd847f807d32b2285885326 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 23 Apr 2016 08:18:33 +0800 Subject: [PATCH 0613/2403] fix style --- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index d06eb6d47f..d3ce57aec0 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -25,6 +25,8 @@ configopts += '--with-netcdf-libs="-lnetcdff -lnetcdf"' buildopts = 'all' +parallel = 1 + files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { @@ -34,5 +36,3 @@ sanity_check_paths = { } moduleclass = 'phys' - -parallel = 1 -- GitLab From cf3fc8237183fa5f3bae7eb7e67089f11f3a4162 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Apr 2016 10:29:18 +0200 Subject: [PATCH 0614/2403] also test with Lmod as modules tool on Travis --- .travis.yml | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index a67e42aebf..82661648a7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,17 @@ language: python -python: - - 2.6 - - 2.7 +python: 2.6 +env: + matrix: + - ENV_MOD_VERSION=3.2.10 + - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod + - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua +matrix: + # mark build as finished as soon as job has failed + fast_finish: true + include: + # also test default configuration with Python 2.7 + - python: 2.7 + env: ENV_MOD_VERSION=3.2.10 addons: apt: packages: @@ -17,7 +27,9 @@ install: - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - - source $(which install_eb_dep.sh) modules-3.2.10 $HOME && source $MOD_INIT + - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi + - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi script: - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From 25e957fafed3d7db1f16375949d364e499a37747 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:09:49 +0200 Subject: [PATCH 0615/2403] long line fix --- .../c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index abd2d674a6..0ddc0b62f9 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -25,8 +25,9 @@ dependencies = [ checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py","bvop","compare_reads","extract_reads","filter_reads","index_and_search"]], - 'dirs' : ['doc','include'] + 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", + "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'dirs' : ['doc', 'include'] } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 92df775e7f99a7067490b356bcf00af058e51f60 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 13:14:34 +0200 Subject: [PATCH 0616/2403] style fixes --- .../Commet-20160422-foss-2016a-Python-2.7.11.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb index 0ddc0b62f9..2c16bccce7 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb @@ -7,7 +7,8 @@ pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' -description = """ COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. +description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of +a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,15 +16,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} # there is no tarball provided, only git checkout through: # https://github.com/pierrepeterlongo/commet/archive/master.zip sources = [SOURCE_ZIP] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] +checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] + +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] dependencies = [ - ('Python', pyver), + ('Python', '2.7.11'), ] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] - sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], -- GitLab From 5576182d21a0dfacf0aa8a1a9b990c254c7cf111 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:08:36 +0200 Subject: [PATCH 0617/2403] quickfixes --- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index f4b92dace0..2abd2af08c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -10,6 +10,8 @@ easyblock = "PythonPackage" name = 'Biopython' version = '1.65' +versionsuffix = "-Python-%(pyver)s" + homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written @@ -22,20 +24,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://biopython.org/DIST'] sources = ['%(namelower)s-%(version)s.tar.gz'] -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%(python)s-%(pyver)s" - dependencies = [ - (python, pyver) + ('Python', '2.7.11') ] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/biopython-%(version)s-py%(pyshortver)s.egg-info'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] } options = {'modulename': 'Bio'} -- GitLab From 2c0e1b6d8ab6bc2727421dc4a8d214a886c2f516 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 23 Apr 2016 19:31:05 +0200 Subject: [PATCH 0618/2403] quickfixes --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb index f798c72eb5..59c924d670 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb @@ -5,11 +5,12 @@ version = '1.4' homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of +gene or protein groups in large biological networks. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True} source_urls = [ 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' @@ -22,11 +23,11 @@ start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3', '', ('foss','2016a'))] +builddependencies = [('CMake', '3.4.3',)] sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 086c0dbb972a7084122b4b5eaf39da87a6bcaacb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 23 Apr 2016 23:56:48 +0100 Subject: [PATCH 0619/2403] Update SAMtools to 1.3.1 --- .../s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 31 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1_Makefile.patch | 24 ++++++++++++++ 4 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb new file mode 100644 index 0000000000..4ee9352c3d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb new file mode 100644 index 0000000000..fea05c529c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb new file mode 100644 index 0000000000..d88f5e50e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-1.3.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch new file mode 100644 index 0000000000..c5b04c6958 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -0,0 +1,24 @@ +Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples +Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile +--- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 ++++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 +@@ -82,13 +82,13 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB)/lib -lz -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3.1#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ +Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc +Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test +Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 2ab4d6d539228f0e637f1e5817cd9b983da10d7b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 24 Apr 2016 19:44:15 +0200 Subject: [PATCH 0620/2403] cutadapt with foss 2016a --- ...cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0a504a247d --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +pyver = '2.7.11' +versionsuffix = '-Python-%(pyver)s' +pyshortver = '.'.join(pyver.split('.')[:2]) + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' -- GitLab From efb8760eacfd270bfefb526017504bc11f0bc3e7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:57:53 +0200 Subject: [PATCH 0621/2403] libgtextutils with foss 2016a --- .../libgtextutils-0.7-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb new file mode 100644 index 0000000000..c1b5b27e46 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/libgtextutils/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' -- GitLab From 7fd4c7a674c4b93466fb96abf122f53e4dc3dbd5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 25 Apr 2016 11:59:57 +0200 Subject: [PATCH 0622/2403] FASTX-Toolket-0.0.14 with foss 2016a --- .../FASTX-Toolkit-0.0.14-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb new file mode 100644 index 0000000000..a69a7b9e2f --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] + +builddependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From ee61831b0499b51bbb5684d61ec1772ffa0c1021 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:00:17 +0200 Subject: [PATCH 0623/2403] Add Clang 3.8 --- .../c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 31 ++++++++++++ .../c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb | 50 +++++++++++++++++++ .../i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 21 ++++++++ .../l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb | 28 +++++++++++ .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 +++++++++++++ .../Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 32 ++++++++++++ .../s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb | 41 +++++++++++++++ 7 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7c4301fdfe --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..23fe1ddcc9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.0" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.0'), + ('ISL', '0.16'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11', '-bare'), + ('libxml2', '2.9.3'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6b38a91f39 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.16' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ba6d0a4c3f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.3' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..02e4aae6ca --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb new file mode 100644 index 0000000000..895d73b128 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.11' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), + # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..5c86155323 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From bfca7b250a70b412b02b70921c158c85923ab215 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Apr 2016 12:57:08 +0200 Subject: [PATCH 0624/2403] Fix conflict --- easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 7c4301fdfe..619aaa3ab8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '6.0'), + ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons #('OpenSSL', '1.0.1s'), -- GitLab From fa805fce3c0dc0dafb44c6c99351fe1d415ace8b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Apr 2016 11:11:25 +0800 Subject: [PATCH 0625/2403] [phys]{intel/2016.02-GCC-4.9} VASP 5.4.1 --- .../VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..f631c4aebb --- /dev/null +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'VASP' +version = '5.4.1' + +homepage = 'http://www.vasp.at' +description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale +materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, +from first principles.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include; ' +prebuildopts += 'env LIBS="" ' + +buildopts = 'all BLACS="$LIBBLACS" ' +buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' + +parallel = 1 + +files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From ebc6dc8fdd062abf4da5cbc1b71570b46f4cc211 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Apr 2016 16:33:46 +0800 Subject: [PATCH 0626/2403] {chem}[intel/2016.02-GCC-4.9] pymatgen 3.5.10 and spglib 1.9.2 --- ...5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 33 +++++++++++++++++++ .../spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 21 ++++++++++++ .../spglib-1.9.2_remove_duplicate.patch | 11 +++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb new file mode 100644 index 0000000000..cacf27ebc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.5.0' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +# source not in url PYPI_SOURCE ? +#source_urls = [PYPI_SOURCE] +source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.9.2'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % py_short_ver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..99c05961d7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.9.2' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['spglib-1.9.2_remove_duplicate.patch'] + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch new file mode 100644 index 0000000000..c228aceb25 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -0,0 +1,11 @@ +--- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 ++++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 +@@ -562,7 +562,7 @@ + version.h + + libsymspg_la_SOURCES = $(spglib_c) $(spglib_h) +-pkginclude_HEADERS = $(spglib_h) debug.h ++pkginclude_HEADERS = $(spglib_h) + # libsymspg_la_LDFLAGS = -version-info 0:1:0 + libsymspg_la_LIBADD = -lm + spglib_test_SOURCES = test.c $(spglib_c) $(spglib_h) -- GitLab From 38ac1422594760bc4281382bd4f22bea36297de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:33:32 +0200 Subject: [PATCH 0627/2403] fix use of resolve_dependencies in tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f3b329c872..db5060f0b6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -113,7 +113,7 @@ class EasyConfigTest(TestCase): if dep.get('external_module', False): ec['dependencies'].remove(dep) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, modules_tool(), retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From 4df336393a0094535ed365c30f094d682a2a9bd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 17:37:38 +0200 Subject: [PATCH 0628/2403] add easyconfig travis-1.8.2-Ruby-2.3.1.eb, add easyconfig Ruby-2.3.1.eb --- easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb | 63 +++++++++++++++++++ .../t/travis/travis-1.8.2-Ruby-2.3.1.eb | 24 +++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb create mode 100644 easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb new file mode 100644 index 0000000000..873541fd42 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb @@ -0,0 +1,63 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.3.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.10', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '1.8.3', ext_options), + ('cabin', '0.8.1', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.0.0', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.9.2', ext_options), + ('faraday_middleware', '0.10.0', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.11.3', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.14.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.8.1', ext_options), + ('typhoeus', '0.8.0', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.4.1', ext_options), + ('rspec-mocks', '3.4.1', ext_options), + ('rspec-expectations', '3.4.0', ext_options), + ('rspec-core', '3.4.4', ext_options), + ('rspec', '3.4.0', ext_options), + ('rack', '1.6.4', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.2', ext_options), + ('sinatra', '1.4.7', ext_options), + ('rack-test', '0.6.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb new file mode 100644 index 0000000000..ebac3ec2d3 --- /dev/null +++ b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb @@ -0,0 +1,24 @@ +easyblock = 'RubyGem' + +name = 'travis' +version = '1.8.2' + +rubyver = '2.3.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/travis-ci/travis.rb' +description = """Travis CI Client (CLI and Ruby library)""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', rubyver)] + +sanity_check_paths = { + 'files': ['bin/travis'], + 'dirs': ['gems/travis-%(version)s/lib/travis'], +} + +moduleclass = 'tools' -- GitLab From 0e7e6ad93bed78ec974e24ad4e697a16f4e6a90c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:37:42 +0200 Subject: [PATCH 0629/2403] install easybuild-framework & easybuild-easyblocks via git clone && easy_install --- .travis.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 82661648a7..00f7860f26 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,10 +22,12 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi - - curl -si https://api.github.com/repos/hpcugent/easybuild-framework/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-framework/archive/${BRANCH}.tar.gz - - curl -si https://api.github.com/repos/hpcugent/easybuild-easyblocks/git/refs/heads/${BRANCH} | grep sha - - easy_install https://github.com/hpcugent/easybuild-easyblocks/archive/${BRANCH}.tar.gz + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git + - cd easybuild-framework; git log -n 1; cd - + - easy_install $PWD/easybuild-framework + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + - cd easybuild-easyblocks; git log -n 1; cd - + - easy_install $PWD/easybuild-easyblocks # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi -- GitLab From 40a6f5d08a0399cc544dd39ba8145a345e4a3414 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2016 19:55:13 +0200 Subject: [PATCH 0630/2403] fix cwd when cloning --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 00f7860f26..127edacd18 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,6 +22,7 @@ install: # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + - cd $HOME - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git - cd easybuild-framework; git log -n 1; cd - - easy_install $PWD/easybuild-framework -- GitLab From fe83740c235f48de4924f02e3a463cce5adc1d68 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:39:01 +0100 Subject: [PATCH 0631/2403] Add patch information and apply more macros --- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb | 4 +++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch | 8 +++----- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb index 4ee9352c3d..a7026c36d0 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '5.9'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb index fea05c529c..7fa65122da 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb index d88f5e50e8..91ca187c34 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -6,6 +6,8 @@ # License:: MIT/GPL # $Id$ # +# Modified by: Adam Huffman +# The Francis Crick Institute ## name = 'SAMtools' version = '1.3.1' @@ -21,7 +23,7 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] # Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-1.3.1_Makefile.patch'] +patches = ['SAMtools-%(version)s_Makefile.patch'] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch index c5b04c6958..4d74b2e9b1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1_Makefile.patch @@ -1,5 +1,6 @@ -Common subdirectories: samtools-1.3.1/examples and samtools-1.3.1.new/examples -Common subdirectories: samtools-1.3.1/htslib-1.3.1 and samtools-1.3.1.new/htslib-1.3.1 +# Use EB modules for zlib and ncurses +# Author: Adam Huffman +# The Francis Crick Institute diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile --- samtools-1.3.1/Makefile 2016-04-22 10:51:16.000000000 +0100 +++ samtools-1.3.1.new/Makefile 2016-04-23 23:53:26.266962157 +0100 @@ -19,6 +20,3 @@ diff -u samtools-1.3.1/Makefile samtools-1.3.1.new/Makefile config.h: echo '/* Basic config.h generated by Makefile */' > $@ -Common subdirectories: samtools-1.3.1/misc and samtools-1.3.1.new/misc -Common subdirectories: samtools-1.3.1/test and samtools-1.3.1.new/test -Common subdirectories: samtools-1.3.1/win32 and samtools-1.3.1.new/win32 -- GitLab From 5145c090f795ab0ef73ae3c6d5b6fe91dc6ab847 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:42:56 +0100 Subject: [PATCH 0632/2403] Second attempt at MuTect update to 1.1.7 --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..fb72a09f73 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Version 1.1.7 modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 41ccd5905b4c848474c5c1744cf05d0b97e607c5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 26 Apr 2016 21:52:42 +0100 Subject: [PATCH 0633/2403] Cleanup macros and provide legacy version --- .../v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 30 +++++++++++++++++++ .../v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 11 +++---- 2 files changed, 36 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..db71fa9969 --- /dev/null +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'JAR' + +name = 'VarScan' +version = '2.3.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://varscan.sourceforge.net/' +description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [('%(name)s.v%(version)s.jar', 'download')] +source_urls = ['https://sourceforge.net/projects/varscan/files/'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index 36d97df090..186dfc58cc 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -6,6 +6,7 @@ easyblock = 'JAR' name = 'VarScan' version = '2.4.1' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/dkoboldt/varscan' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" @@ -15,15 +16,15 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': sources, 'dirs': [], } +modloadmsg = """ +to execute: java -jar \\$EBROOTVARSCAN/VarScan.v%(version)s.jar +""" + moduleclass = 'bio' -- GitLab From 3ccaa14607ffcae465f2e5e94926886fae26a10e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 11:32:39 +0800 Subject: [PATCH 0634/2403] add comments --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index f631c4aebb..1647ef39db 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -11,12 +11,14 @@ from first principles.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} +# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code sources = [SOURCELOWER_TAR_GZ] -prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include; ' -prebuildopts += 'env LIBS="" ' +prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' -buildopts = 'all BLACS="$LIBBLACS" ' +buildopts = 'all LIBS="lib" BLACS="$LIBBLACS" ' + +# override path to libfftw3xf_intel.a buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' parallel = 1 -- GitLab From bede2f51f66ffd99701e4b03c1b94b94a51aaa60 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 11:39:01 +0800 Subject: [PATCH 0635/2403] add comment to patch --- .../easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch index c228aceb25..8382a4ebe3 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2_remove_duplicate.patch @@ -1,3 +1,5 @@ +debug.h is already in $(spglib_h), which causes make install to fail +author: Miguel Dias Costa (National University of Singapore) --- src/Makefile.in.orig 2016-04-26 16:21:29.900203000 +0800 +++ src/Makefile.in 2016-04-26 16:21:43.531192514 +0800 @@ -562,7 +562,7 @@ -- GitLab From c0b8bf724521669e0d3d03746c38ab85d9e3e02d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:05:19 +0800 Subject: [PATCH 0636/2403] use pyshortver template --- .../pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index cacf27ebc3..786e233e0c 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source not in url PYPI_SOURCE ? +# source package not (yet?) in url PYPI_SOURCE #source_urls = [PYPI_SOURCE] source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] sources = [SOURCE_TAR_GZ] @@ -24,10 +24,9 @@ dependencies = [ ('spglib', '1.9.2'), ] -py_short_ver = '.'.join(pythonversion.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages' % py_short_ver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } moduleclass = 'chem' -- GitLab From f716f392e6b4b4c6b613e468d5bf07ab021cbbc2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 12:20:13 +0800 Subject: [PATCH 0637/2403] use && instead of ; between commands --- .../b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index c0d639cc89..5afb842c80 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['8740562da41e87a62eb8d457675e4bfd'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 4700de27c4..9d064dae20 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2'] skipsteps = ['configure'] -prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk; ' +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -- GitLab From 4134e68be75d60ac1889c06af12238baa54fe69b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 Apr 2016 09:20:12 +0200 Subject: [PATCH 0638/2403] Remove redundant easyconfig --- .../n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb deleted file mode 100644 index 02e4aae6ca..0000000000 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ncurses' -version = '6.0' - -homepage = 'http://www.gnu.org/software/ncurses/' -description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, - and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and - function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" - -toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] - -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] - -libs = ["form", "menu", "ncurses", "panel"] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", - "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], -} - -moduleclass = 'devel' -- GitLab From f1a4154428e398d2c45117c91b6cd62af1806829 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 16:31:43 +0800 Subject: [PATCH 0639/2403] fix style --- ...tgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb | 12 +++--------- .../s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb | 2 +- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb index 786e233e0c..f6c2197ee2 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.5.0-intel-2016.02-GCC-4.9-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object @@ -9,18 +10,11 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} -# source package not (yet?) in url PYPI_SOURCE -#source_urls = [PYPI_SOURCE] -source_urls = ['http://pypi.python.org/packages/7a/ae/c1bbe01227514bec203934d608c7319fec173791b3c58afa8e169affb976/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = 'Python' -pythonversion = '2.7.11' - -versionsuffix = '-%s-%s' % (python, pythonversion) - dependencies = [ - (python, pythonversion), + ('Python', '2.7.11'), ('spglib', '1.9.2'), ] diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb index 99c05961d7..8451bf0c50 100644 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.2-intel-2016.02-GCC-4.9.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['spglib-1.9.2_remove_duplicate.patch'] +patches = ['spglib-%(version)s_remove_duplicate.patch'] sanity_check_paths = { 'files': ['lib/libsymspg.a', 'lib/libsymspg.%s' % SHLIB_EXT], -- GitLab From ea2c7c13c4a117b2983cbc8d09bc220672cca07c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 16:56:44 +0800 Subject: [PATCH 0640/2403] explain and cleanup --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 1647ef39db..5a21fc97d7 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -16,10 +16,13 @@ sources = [SOURCELOWER_TAR_GZ] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' -buildopts = 'all LIBS="lib" BLACS="$LIBBLACS" ' +# path to libfftw3xf_intel.a is hardcoded in makefile.include +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$FFTW_LIB_DIR|" makefile.include && ' -# override path to libfftw3xf_intel.a -buildopts += 'OBJECTS="fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $FFTW_LIB_DIR/libfftw3xf_intel.a"' +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +buildopts = 'all BLACS="$LIBBLACS" ' parallel = 1 -- GitLab From 435eab2e07d7f781915cb672792e3ed0506dfa96 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 10:04:20 +0100 Subject: [PATCH 0641/2403] Don't specify version for dummy toolchain --- easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index db71fa9969..ba30d5877f 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -11,7 +11,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://varscan.sourceforge.net/' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = [('%(name)s.v%(version)s.jar', 'download')] source_urls = ['https://sourceforge.net/projects/varscan/files/'] -- GitLab From a9193aaca3032ffc844843556cba05e5957a3382 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:17 +0200 Subject: [PATCH 0642/2403] add easyconfig netCDF-Fortran-4.4.3-intel-2016a.eb --- .../netCDF-Fortran-4.4.3-intel-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb new file mode 100644 index 0000000000..4b898dd0fe --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'netCDF-Fortran' +version = '4.4.3' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-fortran/archive/' +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From 0ff3e40f352c19ec30bc19fac917588e318ba4fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:38:47 +0200 Subject: [PATCH 0643/2403] add easyconfig tcsh-6.19.00-intel-2016a.eb --- .../t/tcsh/tcsh-6.19.00-intel-2016a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb new file mode 100644 index 0000000000..4a02bab4b4 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.19.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 45e20dbc351d80c93701dfc2fa9231d99019607f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 11:39:16 +0200 Subject: [PATCH 0644/2403] add easyconfig JasPer-1.900.1-intel-2016a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb new file mode 100644 index 0000000000..ea3c592427 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 7f79c14c4dcfd9d7aa02352f8bdc537325276a25 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Apr 2016 17:51:09 +0800 Subject: [PATCH 0645/2403] fix variable --- .../easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 5a21fc97d7..2a6923ac23 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include -prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$FFTW_LIB_DIR|" makefile.include && ' +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' # VASP uses LIBS as a list of folders prebuildopts += 'unset LIBS && ' -- GitLab From 7f749b704350f3618123f17349c3b2599408bbbd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 11:56:43 +0100 Subject: [PATCH 0646/2403] Use new download URL and apply new Java macros to existing 1.1.4 easyconfig --- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 15 ++++---- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 37 ------------------- 2 files changed, 8 insertions(+), 44 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 1434f1c176..b7e4fa9091 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -2,11 +2,15 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute easyblock = 'Tarball' name = 'MuTect' version = '1.1.4' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' description = """ MuTect is a method developed at the Broad Institute for the reliable @@ -15,14 +19,11 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} -source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +# Need to be logged in to download, at this URL +# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] sources = ['muTect-%(version)s-bin.zip'] -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_80')] sanity_check_paths = { 'files': ["muTect-%(version)s.jar"], @@ -30,7 +31,7 @@ sanity_check_paths = { } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb deleted file mode 100644 index fb72a09f73..0000000000 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Version 1.1.7 modified by -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'Tarball' - -name = 'MuTect' -version = '1.1.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' -description = """ MuTect is a method developed at the Broad Institute for the reliable - and accurate identification of somatic point mutations in next generation sequencing - data of cancer genomes. """ - -toolchain = {'name': 'dummy', 'version': ''} - -# Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] -sources = ['muTect-%(version)s-bin.zip'] - -dependencies = [('Java', '1.7.0_80')] - -sanity_check_paths = { - 'files': ["muTect-%(version)s.jar"], - 'dirs': [], -} - -modloadmsg = """ -To start MuTect: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar -""" - -moduleclass = 'bio' -- GitLab From 836bced923277203a737f146a839a8fd491ea0cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:39:28 +0200 Subject: [PATCH 0647/2403] add easyconfig ParMETIS-4.0.3-intel-2016a.eb, add easyconfig METIS-5.1.0-intel-2016a-32bitIDX.eb, add easyconfig SCOTCH-6.0.4-intel-2016a.eb, add easyconfig ParMGridGen-1.0-intel-2016a.eb, add easyconfig OpenFOAM-Extend-3.2-intel-2016a.eb, add easyconfig numactl-2.0.11-intel-2016a.eb, add easyconfig hwloc-1.11.3-intel-2016a.eb --- .../h/hwloc/hwloc-1.11.3-intel-2016a.eb | 23 +++++++++ .../METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb | 24 ++++++++++ .../n/numactl/numactl-2.0.11-intel-2016a.eb | 23 +++++++++ .../OpenFOAM-Extend-3.2-intel-2016a.eb | 48 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb | 22 +++++++++ .../ParMGridGen-1.0-intel-2016a.eb | 27 +++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 14 ++++++ 7 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb new file mode 100644 index 0000000000..aad28dd23b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb new file mode 100644 index 0000000000..a9aa0626e9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016a-32bitIDX.eb @@ -0,0 +1,24 @@ +name = 'METIS' +version = '5.1.0' +# default 32-bit IDTYPEWIDTH, no patch used +versionsuffix = '-32bitIDX' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb new file mode 100644 index 0000000000..6379096747 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb new file mode 100644 index 0000000000..00e9eaf007 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +version = '3.2' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'OpenFOAM-Extend-%(version)s-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-3.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', +] + +dependencies = [ + ('hwloc', '1.11.3'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0', '-32bitIDX'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '6.0.4'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.11'), + # Libccmio v2.6.1, zoltan v3.5 +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('M4', '1.4.17'), + ('CMake', '3.5.2'), +] + +prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb new file mode 100644 index 0000000000..d1d34fb057 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb new file mode 100644 index 0000000000..081f188ad5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] +sources = [SOURCE_TAR_GZ] + +patches = ['ParMGridGen-1.0_malloc_include.patch'] + +buildopts = 'parallel CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h'], 'include'), + (['libmgrid.a', 'libparmgrid.a'], 'lib'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb new file mode 100644 index 0000000000..a90bb75fa5 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From 34b5d5abfa255f3464ce6dabefc279d14b2b67e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 13:44:11 +0200 Subject: [PATCH 0648/2403] add easyconfig JAGS-4.2.0-intel-2016a.eb --- .../j/JAGS/JAGS-4.2.0-intel-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000..1474dde18b --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' -- GitLab From cb092140059005c5fc0468dfb57ad2b5b4f04726 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 14:03:24 +0200 Subject: [PATCH 0649/2403] add easyconfig Mesquite-2.3.0-intel-2016a.eb --- .../m/Mesquite/Mesquite-2.3.0-intel-2016a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb new file mode 100644 index 0000000000..fd518b2227 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2016a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' -- GitLab From 7bb25d33b0db30e01c8e995fdc0c3c4df76a5769 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 14:13:13 +0100 Subject: [PATCH 0650/2403] Clean up download URL --- easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index b7e4fa9091..0d2d28d47b 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -20,7 +20,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} # Need to be logged in to download, at this URL -# source_urls = ['http://www.broadinstitute.org/cancer/cga/mutect_download'] +# http://www.broadinstitute.org/cancer/cga/mutect_download sources = ['muTect-%(version)s-bin.zip'] dependencies = [('Java', '1.7.0_80')] -- GitLab From 7706f3436e6b061846889c767616bfb3dbce8478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 15:53:30 +0200 Subject: [PATCH 0651/2403] {geo}[intel/2016a] WRF 3.8 --- .../w/WRF/WRF-3.8-intel-2016a-dmpar.eb | 39 +++ ...F-3.8.0_netCDF-Fortran_separate_path.patch | 225 ++++++++++++++++++ 2 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb new file mode 100644 index 0000000000..8afc4ff822 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.19.00')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 0000000000..f46ae78e87 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,225 @@ +add support for using netCDF and netCDF-Fortran installations in separate paths +author: Kenneth Hoste (HPC-UGent) +diff -ru WRFV3.orig/arch/Config_new.pl WRFV3/arch/Config_new.pl +--- WRFV3.orig/arch/Config_new.pl 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/arch/Config_new.pl 2016-04-27 12:07:59.419553000 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib may be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -87,6 +88,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -114,6 +119,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -417,6 +423,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +Only in WRFV3/arch: Config_new.pl.orig +diff -ru WRFV3.orig/arch/configure_new.defaults WRFV3/arch/configure_new.defaults +--- WRFV3.orig/arch/configure_new.defaults 2016-02-29 07:22:29.000000000 +0100 ++++ WRFV3/arch/configure_new.defaults 2016-04-27 12:07:59.429182000 +0200 +@@ -1626,6 +1626,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +Only in WRFV3/arch: configure_new.defaults.orig +diff -ru WRFV3.orig/arch/conf_tokens WRFV3/arch/conf_tokens +--- WRFV3.orig/arch/conf_tokens 2008-02-26 16:39:38.000000000 +0100 ++++ WRFV3/arch/conf_tokens 2016-04-27 12:07:59.435906000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -ru WRFV3.orig/arch/postamble_new WRFV3/arch/postamble_new +--- WRFV3.orig/arch/postamble_new 2016-02-05 22:22:09.000000000 +0100 ++++ WRFV3/arch/postamble_new 2016-04-27 12:08:58.368686000 +0200 +@@ -45,6 +45,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ + -I$(NETCDFPATH)/include \ ++ -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -67,6 +68,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH +++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + PNETCDFPATH = CONFIGURE_PNETCDF_PATH +@@ -97,7 +99,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +Only in WRFV3/arch: postamble_new.orig +Only in WRFV3/arch: postamble_new.rej +diff -ru WRFV3.orig/configure WRFV3/configure +--- WRFV3.orig/configure 2015-12-11 19:38:11.000000000 +0100 ++++ WRFV3/configure 2016-04-27 12:58:24.475136000 +0200 +@@ -287,16 +287,28 @@ + USENETCDFF="" # see below + if [ -n "$NETCDF" ] ; then + echo "Will use NETCDF in dir: $NETCDF" ++ # for netCDF 4.2 and greater, the Fortran library is a separate install ++ if [ -z "$NETCDFF" ]; then ++ NETCDFF="$NETCDFF" ++ fi + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi + if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else +- USENETCDF=" " ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space ++ else ++ USENETCDF=" " ++ fi + fi + else + echo "Will configure for use without NetCDF" +@@ -595,7 +607,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure_new.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config_new.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -707,10 +719,10 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure_new.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + echo + if test -n "$NETCDF4" ; then +@@ -719,7 +731,7 @@ + fi + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +Only in WRFV3: configure.orig +Only in WRFV3: configure.rej +diff -ru WRFV3.orig/external/io_netcdf/makefile WRFV3/external/io_netcdf/makefile +--- WRFV3.orig/external/io_netcdf/makefile 2014-07-13 01:39:10.000000000 +0200 ++++ WRFV3/external/io_netcdf/makefile 2016-04-27 12:07:59.490731000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -ru WRFV3.orig/Makefile WRFV3/Makefile +--- WRFV3.orig/Makefile 2016-03-11 18:47:37.000000000 +0100 ++++ WRFV3/Makefile 2016-04-27 12:09:30.391608000 +0200 +@@ -867,7 +867,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) framework; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" FC="$(FC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" FC="$(SFC) $(FCBASEOPTS)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ + ESMF_MOD_DEPENDENCE="$(ESMF_MOD_DEPENDENCE)" AR="INTERNAL_BUILD_ERROR_SHOULD_NOT_NEED_AR" diffwrf; \ +Only in WRFV3: Makefile.orig +Only in WRFV3: Makefile.rej -- GitLab From 4734e785722c5b78cd0fe7420776439273e22727 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2016 16:14:00 +0200 Subject: [PATCH 0652/2403] fix easyconfig filename --- ...RF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/w/WRF/{WRF-3.8-intel-2016a-dmpar.eb => WRF-3.8.0-intel-2016a-dmpar.eb} (100%) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.8-intel-2016a-dmpar.eb rename to easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016a-dmpar.eb -- GitLab From 39ddf5a97d55a5b9248c9bf3916d1b9fb41f8513 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2016 15:14:27 +0100 Subject: [PATCH 0653/2403] Update MuTect for 1.1.7 from new download site --- .../m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb new file mode 100644 index 0000000000..86bd5019e2 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +# Need to be logged in to download, at this URL +# and to click the checkbox to agree to the licence +# https://www.broadinstitute.org/gatk/download/auth?package=MuTect +sources = ['%(namelower)s-%(version)s.jar.zip'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["%(namelower)s-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +To start MuTect: java -jar \\$EBROOTMUTECT/%(namelower)s-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From bc263b4af815e026b5f205a443e4acb83d39e66b Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 27 Apr 2016 23:56:45 -0400 Subject: [PATCH 0654/2403] changing minieigen easyconfig --- ...-2016a.eb => minieigen-0.5.3-foss-2016a-Python-2.7.11.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/minieigen/{minieigen-0.5.3-foss-2016a.eb => minieigen-0.5.3-foss-2016a-Python-2.7.11.eb} (86%) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb similarity index 86% rename from easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb rename to easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index 4a8f2d9f28..bc907e8f48 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -21,10 +21,9 @@ dependencies = [ ('Python', '2.7.11'), ] -#incomplete sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [] } moduleclass = 'lib' -- GitLab From 6731122a46e0039315726eb9b9b25c089ae83c62 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Thu, 28 Apr 2016 00:10:40 -0400 Subject: [PATCH 0655/2403] Update minieigen-0.5.3-foss-2016a-Python-2.7.11.eb --- .../m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index bc907e8f48..bcc3a6db18 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], - 'dirs': [] + 'dirs': [], } moduleclass = 'lib' -- GitLab From 0034a297d2af91edbdc0eb9d83903219ec07c612 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 02:41:08 -0400 Subject: [PATCH 0656/2403] add GTS easyconfig dependency and improve yade easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 25 +++++++++++++++++++ .../y/Yade/Yade-1.20.0-foss-2016a.eb | 22 ++++++++-------- 2 files changed, 36 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000..6e89234d6b --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb index 83be6ba55d..11f2219023 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb @@ -14,21 +14,23 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' +suffix = '-Python-%(pyver)s' dependencies = [ ('Loki', '0.1.7'), - ('Boost', '1.60.0', versionsuffix), -# ('IPython', '3.2.3', versionsuffix), + ('Boost', '1.60.0', suffix), + ('GL2PS', '1.3.9'), + ('IPython', '3.2.3', suffix), # ('matplotlib', '1.5.1'), # ('SQLite', '3.9.2'), - ('numpy', '1.8.2', versionsuffix), + ('numpy', '1.8.2', suffix), ('Eigen', '3.2.7'), - ('minieigen', '0.5.3') + ('minieigen', '0.5.3', suffix), ('Qt', '4.8.7'), + ('GTS', '0.7.6'), ('Python', '2.7.11'), -# ('libQGLViewer', '2.6.3'), -# ('GDB', '7.10.1',versionsuffix), + ('libQGLViewer', '2.6.3'), +# ('GDB', '7.10.1',suffix), # optional # ('VTK', '6.3.0'), # ('CGAL', '4.7'), @@ -68,11 +70,9 @@ configopts += '-DENABLE_PFVFLOW=OFF' # VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) # USE_QT5: use QT5 for GUI, experimental (OFF by default) - -#incomplete sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch'], - 'dirs': ["."] + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'dirs': ['lib/x86_64-linux-gnu/yade-%(versio)s/py/yade'], } moduleclass = 'devel' -- GitLab From c923c1dab8db1edae7d3ee6f6351bccd59f953b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 28 Apr 2016 16:24:03 +0800 Subject: [PATCH 0657/2403] {chem}[intel/2016.02-GCC-4.9] QuantumESPRESSO 5.3.0 --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..91045a89e8 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'QuantumESPRESSO' +version = '5.3.0' + +homepage = 'http://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://qe-forge.org/gf/download/frsrelease/204/912/'] +sources = ['espresso-%(version)s.tar.gz'] +checksums = ['6848fcfaeb118587d6be36bd10b7f2c3'] + +configopts = 'DFLAGS="-D__INTEL -D__MPI -D__PARA -D__DFTI -D__SCALAPACK" ' +configopts += 'FFT_LIBS="$LIBFFT" --with-scalapack=intel ' +configopts += '--prefix=%(installdir)s/bin' + +buildopts = 'all' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/' + prog for prog in ['average.x', 'bands.x', 'bgw2pw.x', 'cppp.x', + 'cp.x', 'd3.x', 'dist.x', 'dos.x', 'dynmat.x', 'epsilon.x', 'ev.x', 'fd_ef.x', + 'fd_ifc.x', 'fd.x', 'fqha.x', 'fs.x', 'generate_rVV10_kernel_table.x', + 'generate_vdW_kernel_table.x', 'importexport_binary.x', 'initial_state.x', + 'iotk_print_kinds.x', 'iotk.x', 'kpoints.x', 'lambda.x', 'ld1.x', + 'manypw.x', 'matdyn.x', 'molecularpdos.x', 'neb.x', 'path_interpolation.x', + 'phcg.x', 'ph.x', 'plan_avg.x', 'plotband.x', 'plotproj.x', 'plotrho.x', + 'pmw.x', 'pp.x', 'projwfc.x', 'pw2bgw.x', 'pw2gw.x', 'pw2wannier90.x', + 'pwcond.x', 'pw_export.x', 'pwi2xsf.x', 'pw.x', 'q2qstar.x', 'q2r.x', + 'q2trans_fd.x', 'q2trans.x', 'spectra_manipulation.x', 'sumpdos.x', + 'turbo_davidson.x', 'turbo_eels.x', 'turbo_lanczos.x', 'turbo_spectrum.x', + 'wannier_ham.x', 'wannier_plot.x', 'wfck2r.x', 'wfdd.x', 'xspectra.x']], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 16218db65d867ab958db13dcbe99fcbf93724337 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:32:51 +0200 Subject: [PATCH 0658/2403] add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs --- .../i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 9 +++++++++ .../i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 693b2889a6..440fcbb412 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index e3341fcf31..7cf61546f1 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -52,9 +52,18 @@ exts_list = [ ('tornado', '4.3', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From d5d14e4f772188d6772c1dd9f3453ccc2725845c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:28:48 +0200 Subject: [PATCH 0659/2403] add vcversioner and functiools32 dependencies for jsonscheme in IPython easyconfig --- .../i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb index f70668f24c..5a7a6fc6ee 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2016a-Python-2.7.11.eb @@ -50,10 +50,16 @@ exts_list = [ }), ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - }), + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], }), -- GitLab From 364ccf36a72ed191b8641e62239e7f924f228a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2016 11:35:26 +0200 Subject: [PATCH 0660/2403] use %(pyver)s and %(pyshortver)s in IPython 3.2.3 easyconfigs --- .../IPython-3.2.3-foss-2015a-Python-2.7.11.eb | 12 ++++-------- .../IPython-3.2.3-intel-2015b-Python-2.7.10.eb | 12 ++++-------- 2 files changed, 8 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb index 440fcbb412..59f875819a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.11'), ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb index 7cf61546f1..4c8be19f1d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015b-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015b'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), ('PyZMQ', '15.1.0', '%s-zmq4' % versionsuffix), ] @@ -82,11 +78,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ -- GitLab From 699e52ba961e329166861b28967659ef5284534b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:51:54 +0200 Subject: [PATCH 0661/2403] dropped (new)lines --- .../c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 0a504a247d..5c57e5846c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -9,9 +9,7 @@ easyblock = "PythonPackage" name = 'cutadapt' version = '1.9.1' -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' -pyshortver = '.'.join(pyver.split('.')[:2]) homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and @@ -22,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From 4b3f26cdb67eae384e941d5a9358502f27376475 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 14:55:11 +0200 Subject: [PATCH 0662/2403] Version fix --- .../c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb new file mode 100644 index 0000000000..444de341bf --- /dev/null +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CrossTalkZ' +version = '1.4' + +homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +description = """ +CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment +between pairs of gene or protein groups in large biological networks. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' +] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('Boost', '1.60.0')] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" + +builddependencies = [('CMake', '3.4.3',)] + +sanity_check_paths = { + 'files': ['bin/CrossTalkZ'], + 'dirs': [''], +} + +moduleclass = 'bio' -- GitLab From 1f5400281627eb85afc587878f025e95fe58e9d5 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 10:37:28 -0400 Subject: [PATCH 0663/2403] remove easyblock specification. it's not necessary --- .../easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb index cd9274f066..7bcbf378aa 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_libQGLViewer' - name = 'libQGLViewer' version = '2.6.3' -- GitLab From 4b632a70fb083454a252435f93947990715fce77 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 28 Apr 2016 16:42:26 +0200 Subject: [PATCH 0664/2403] remove 1.0 version --- .../c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb deleted file mode 100644 index 59c924d670..0000000000 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.0-foss-2016a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'CrossTalkZ' -version = '1.4' - -homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -description = """ -CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of -gene or protein groups in large biological networks. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [ - 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/' -] -sources = ['%(name)s_%(version)s.tgz'] - -dependencies = [('Boost', '1.60.0')] - -start_dir = 'src' - -configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" - -builddependencies = [('CMake', '3.4.3',)] - -sanity_check_paths = { - 'files': ['bin/CrossTalkZ'], - 'dirs': [''], -} - -moduleclass = 'bio' -- GitLab From 191c0834d484b49927c15006879a7a6266d9253e Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 15:01:15 -0400 Subject: [PATCH 0665/2403] improve Loki and minieigen easyconfig files --- easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb | 4 ++-- .../easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch | 9 --------- .../easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch | 4 ++-- 3 files changed, 4 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index dcb7370cfb..990683c5b7 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -8,7 +8,7 @@ description = """ Loki is a C++ library of designs, containing flexible implemen toolchain = {'name': 'foss', 'version': '2016a'} -preinstallopts = "export EB_INSTALL_DIR=%(installdir)s &&" +installopts = "prefix=%(installdir)s" source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] sources = [SOURCELOWER_TAR_GZ] @@ -20,4 +20,4 @@ sanity_check_paths={ 'dirs': ['include/loki'], } -patches = [('Loki-0.1.7_change_prefix.patch')] +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch b/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch deleted file mode 100644 index 8a0666c803..0000000000 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7_change_prefix.patch +++ /dev/null @@ -1,9 +0,0 @@ -diff -ru loki-0.1.7.orig/Makefile.common loki-0.1.7/Makefile.common ---- loki-0.1.7.orig/Makefile.common 2007-05-28 22:26:26.000000000 -0400 -+++ loki-0.1.7/Makefile.common 2016-04-21 18:20:54.280476472 -0400 -@@ -4,4 +4,4 @@ - CXXWARNFLAGS := -Wall -Wold-style-cast -Wundef -Wsign-compare -Wconversion -Wpointer-arith -pedantic - CXXFLAGS := $(CXXWARNFLAGS) -g -O2 - --prefix := /usr -+prefix := $(EB_INSTALL_DIR) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch index 2d683420ff..95775909f2 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch @@ -1,6 +1,6 @@ diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py --- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 -+++ minieigen-0.5.3/setup.py 2016-04-22 15:34:16.527587398 -0400 ++++ minieigen-0.5.3/setup.py 2016-04-28 14:12:46.507198765 -0400 @@ -1,6 +1,6 @@ # encoding: utf-8 from distutils.core import setup,Extension @@ -13,7 +13,7 @@ diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py # * https://bugs.launchpad.net/panda3d/+bug/919237 define_macros+=[('EIGEN_DONT_VECTORIZE',None)] else: -+ eigen_prefix = os.environ["EBROOTEIGEN"] ++ eigen_prefix = os.environ.get('EBROOTEIGEN', 'EBROOTEIGEN_NOT_DEFINED') py3k=(sys.version_info[0]==3) libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] library_dirs=[] -- GitLab From 34c2d2a3f23f82a1584528664c4efd174ffd5c04 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 28 Apr 2016 23:22:11 +0100 Subject: [PATCH 0666/2403] add easyconfig cramtools-3.0-Java-1.7.0_80.eb --- .../cramtools/cramtools-3.0-Java-1.7.0_80.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..d00a912e71 --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '3.0' +versionsuffix = "-Java-%(javaver)s" + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +dependencies = [('Java', '1.7.0_80')] + +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' -- GitLab From 942f96a8f5f8a5b8b2586aa101d78ab815598490 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 28 Apr 2016 22:18:01 -0400 Subject: [PATCH 0667/2403] add PyGTS easyconfig with foss 2016a toolchain --- .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..d74951a2d3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.47.5'), + ('GTS' ,'0.7.6'), + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' -- GitLab From 38eb196e7de2b754a1c0205e11df8a50d9b2075b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 15:30:02 +0200 Subject: [PATCH 0668/2403] add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used --- ...tplotlib-1.5.1-foss-2015b-Python-2.7.10.eb | 1 + ...tplotlib-1.5.1-foss-2016a-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2015b-Python-2.7.11.eb | 1 + ...plotlib-1.5.1-intel-2016a-Python-2.7.11.eb | 1 + ...tplotlib-1.5.1-intel-2016a-Python-3.5.1.eb | 1 + .../matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch | 26 +++++++++++++++++++ 6 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb index 712519a60c..96e332c757 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2015b-Python-2.7.10.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb index 182905c4bb..a29279c43f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb index 8b047bb737..790acc6037 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2015b-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb index 551c06ecef..0e7eed5918 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11.eb @@ -28,6 +28,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb index 2c2c674d2c..8f02974208 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-3.5.1.eb @@ -29,6 +29,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch new file mode 100644 index 0000000000..39e34a937a --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch @@ -0,0 +1,26 @@ +ensure that Tcl/Tk library paths are correct, to fix segmentation fault that occurs when plotting because system +libraries are picked up; +the problem is that the query_tcktl method guesses the Tk library path based on the Tcl library path by simply +replacing 'Tcl'/'tcl' with 'Tk'/'tk', which doesn't work if the Tk install prefix is different (e.g. due to a +versionsuffix) +author: Kenneth Hoste (HPC-UGent) +-- matplotlib-1.5.1.orig/setupext.py 2016-01-11 04:06:08.000000000 +0100 ++++ matplotlib-1.5.1/setupext.py 2016-04-29 15:43:21.280170000 +0200 +@@ -1560,7 +1560,16 @@ + + # Query Tcl/Tk system for library paths and version string + try: +- tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() ++ tcl_lib_dir, tk_lib_dir, tk_ver = None, None, None ++ if 'EBROOTTCL' in os.environ and 'EBVERSIONTCL' in os.environ: ++ tcl_ver = '.'.join(os.environ['EBVERSIONTCL'].split('.')[:2]) ++ tcl_lib_dir = os.path.join(os.environ['EBROOTTCL'], 'lib', 'tcl%s' % tcl_ver) ++ if 'EBROOTTK' in os.environ and 'EBVERSIONTK' in os.environ: ++ tk_ver = '.'.join(os.environ['EBVERSIONTK'].split('.')[:2]) ++ tk_lib_dir = os.path.join(os.environ['EBROOTTK'], 'lib', 'tk%s' % tk_ver) ++ ++ if tcl_lib_dir is None or tk_lib_dir is None or tk_ver is None: ++ tcl_lib_dir, tk_lib_dir, tk_ver = self.query_tcltk() + except: + tk_ver = '' + result = self.hardcoded_tcl_config() -- GitLab From a2850e36d1656a502b69931419974015537c8ab3 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 10:08:49 -0400 Subject: [PATCH 0669/2403] add GTS easyconfig and improve PyGTS easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 25 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 1 - 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb new file mode 100644 index 0000000000..6e89234d6b --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.47.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index d74951a2d3..9d7551949d 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,6 @@ dependencies = [ ('Python', '2.7.11'), ('GLib', '2.47.5'), ('GTS' ,'0.7.6'), - ('numpy', '1.8.2', versionsuffix), ] options = {'modulename': 'gts'} -- GitLab From 6a2282637a078b69ace9f82d62765e22779c1241 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 11:02:01 -0400 Subject: [PATCH 0670/2403] improve Yade easyconfig --- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5e5fa25372 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,74 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Loki', '0.1.7'), + ('Boost', '1.60.0', versionsuffix), + ('GL2PS', '1.3.9'), + ('Python', '2.7.11'), + ('IPython', '3.2.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Eigen', '3.2.7'), + ('minieigen', '0.5.3', versionsuffix), + ('Qt', '4.8.7'), + ('GTS', '0.7.6'), + ('libQGLViewer', '2.6.3'), + ('GDB', '7.10.1', versionsuffix), + ('zlib', '1.2.8'), + # optional +# ('CGAL', '4.7'), +] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF ' +configopts += '-DENABLE_VTK=OFF ' +configopts += '-DENABLE_CGAL=OFF' +configopts += '-DENABLE_LINSOLV=OFF ' +configopts += '-DENABLE_PFVFLOW=OFF ' +configopts += '-DQGLVIEWER_INCLUDE_DIR=$EBROOTLIBQGLVIEWER/include ' + +# In case you want disable some Yade features +# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' + +# options available, +# ENABLE_GUI: enable GUI option (ON by default) +# ENABLE_CGAL: enable CGAL option (ON by default) +# ENABLE_VTK: enable VTK-export option (ON by default) +# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) +# ENABLE_GTS: enable GTS-option (ON by default) +# ENABLE_GL2PS: enable GL2PS-option (ON by default) +# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) +# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) +# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) +# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) +# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) +# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) +# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) +# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) +# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) +# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) +# USE_QT5: use QT5 for GUI, experimental (OFF by default) + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], +} + +moduleclass = 'devel' -- GitLab From be83e907e89d1d3ac81cc14416412fb4ee9f9c58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:05 +0200 Subject: [PATCH 0671/2403] add easyconfig MPFR-3.1.4-intel-2016a.eb --- .../m/MPFR/MPFR-3.1.4-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb new file mode 100644 index 0000000000..6101f2969d --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 3cd38ae9e6ddbf1c0541b9aab0c608dc4976e654 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:23:26 +0200 Subject: [PATCH 0672/2403] add easyconfig GLib-2.48.0-intel-2016a.eb, add easyconfig gettext-0.19.7-intel-2016a.eb --- .../g/GLib/GLib-2.48.0-intel-2016a.eb | 33 +++++++++++++++++++ .../g/gettext/gettext-0.19.7-intel-2016a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb new file mode 100644 index 0000000000..6f5acf6419 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb new file mode 100644 index 0000000000..d256bae534 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' -- GitLab From b9b61a1d3edfbc23b79c5c001ee8a03bf8e584cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:26:30 +0200 Subject: [PATCH 0673/2403] add easyconfig Mesa-11.2.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb, add easyconfig pkg-config-0.29.1-intel-2016a.eb, add easyconfig libdrm-2.4.68-intel-2016a.eb, add easyconfig libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb --- ...bXfont-1.5.1-intel-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-intel-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-intel-2016a.eb | 68 +++++++++++++++++++ .../pkg-config-0.29.1-intel-2016a.eb | 27 ++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..45a31bc1bd --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb new file mode 100644 index 0000000000..e64ac66c51 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb new file mode 100644 index 0000000000..54f7d8a513 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb new file mode 100644 index 0000000000..eeb50eabb1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From eadd15710a076003297e0f6a504471fb0352c211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:23 +0200 Subject: [PATCH 0674/2403] add easyconfig xcb-util-0.4.0-intel-2016a.eb, add easyconfig xcb-util-image-0.4.0-intel-2016a.eb, add easyconfig xcb-util-keysyms-0.4.0-intel-2016a.eb, add easyconfig xcb-util-renderutil-0.3.9-intel-2016a.eb, add easyconfig xcb-util-wm-0.4.1-intel-2016a.eb --- .../xcb-util-image-0.4.0-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-keysyms-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 23 ++++++++++++++++++ .../xcb-util-wm-0.4.1-intel-2016a.eb | 23 ++++++++++++++++++ .../x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 24 +++++++++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..a0cf9f13dd --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..ab965a9d36 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb new file mode 100644 index 0000000000..c926c17dd1 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb new file mode 100644 index 0000000000..5d58f2a9b2 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb new file mode 100644 index 0000000000..18a587a56e --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 5a09c330918abdab2e6129d2c9767a6a29b3b704 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:37:45 +0200 Subject: [PATCH 0675/2403] add easyconfig fontconfig-2.11.95-intel-2016a.eb, add easyconfig expat-2.1.1-intel-2016a.eb, modify easyconfig freetype-2.6.3-intel-2016a.eb --- .../e/expat/expat-2.1.1-intel-2016a.eb | 16 ++++++++++++++ .../fontconfig-2.11.95-intel-2016a.eb | 22 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a442e3de7f --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb new file mode 100644 index 0000000000..09b5a49088 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 88739b6f181046a73e49da989652c1cd433c6d9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:42:32 +0200 Subject: [PATCH 0676/2403] add easyconfig Qt5-5.6.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb, add easyconfig libxkbcommon-0.6.1-intel-2016a.eb, add easyconfig XKeyboardConfig-2.17-intel-2016a.eb, add easyconfig libxslt-1.1.28-intel-2016a.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++ .../libxkbcommon-0.6.1-intel-2016a.eb | 32 +++++++++++++++ .../l/libxslt/libxslt-1.1.28-intel-2016a.eb | 24 ++++++++++++ .../q/Qt5/Qt5-5.6.0-intel-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-intel-2016a.eb | 36 +++++++++++++++++ 5 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb new file mode 100644 index 0000000000..8611f0332b --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb new file mode 100644 index 0000000000..b3d064b443 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb new file mode 100644 index 0000000000..f4f0ab35bd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb new file mode 100644 index 0000000000..e72178d939 --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' -- GitLab From d6ed5a22d8156e7fec24f3a3865afa0cb59ba4c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 21:44:07 +0200 Subject: [PATCH 0677/2403] bump to CGAL 4.8 using Mesa 11.2.1 as dependency --- ...1.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/c/CGAL/{CGAL-4.7-intel-2016a-Python-2.7.11.eb => CGAL-4.8-intel-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb index 1e7bf4a653..fd4219e206 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ name = 'CGAL' -version = '4.7' +version = '4.8' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.cgal.org/' @@ -12,17 +12,14 @@ toolchainopts = {'strict': True} # note: source URL needs to be updated for a new version (checksums too)! source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['623d91fb2ab0a35049dc6098a0f235cc'] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] - -mesaver = '11.1.2' dependencies = [ ('Python', '2.7.11'), ('Boost', '1.60.0', versionsuffix), - ('MPFR', '3.1.3', '-GMP-6.1.0'), - ('Qt5', '5.5.1', '-Mesa-%s' % mesaver), - ('Mesa', mesaver, versionsuffix), - ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " @@ -30,7 +27,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT builddependencies = [ - ('CMake', '3.4.1'), + ('CMake', '3.5.2'), ] moduleclass = 'numlib' -- GitLab From 73c8947bf09632f27010a1a8cd8ea77afa5e73d9 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 16:07:15 -0400 Subject: [PATCH 0678/2403] I forgot to remove the old easyconfig file --- .../y/Yade/Yade-1.20.0-foss-2016a.eb | 78 ------------------- 1 file changed, 78 deletions(-) delete mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb deleted file mode 100644 index 11f2219023..0000000000 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a.eb +++ /dev/null @@ -1,78 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Yade' -version = '1.20.0' - -homepage = 'https://yade-dem.org/doc/' -description = """ Yade is an extensible open-source framework for discrete numerical models, - focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, - allowing independent implementation of new alogrithms and interfaces. - Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] -sources = [SOURCELOWER_TAR_GZ] - -suffix = '-Python-%(pyver)s' - -dependencies = [ - ('Loki', '0.1.7'), - ('Boost', '1.60.0', suffix), - ('GL2PS', '1.3.9'), - ('IPython', '3.2.3', suffix), -# ('matplotlib', '1.5.1'), -# ('SQLite', '3.9.2'), - ('numpy', '1.8.2', suffix), - ('Eigen', '3.2.7'), - ('minieigen', '0.5.3', suffix), - ('Qt', '4.8.7'), - ('GTS', '0.7.6'), - ('Python', '2.7.11'), - ('libQGLViewer', '2.6.3'), -# ('GDB', '7.10.1',suffix), - # optional -# ('VTK', '6.3.0'), -# ('CGAL', '4.7'), -# ('SuiteSparse', '4.5.1'), -# ('OpenBLAS', '0.2.15'), -# ('METIS', '5.1.0'), -] - -builddependencies = [('CMake', '3.4.3')] - -separate_build_dir = True - -configopts = '-DENABLE_GUI=OFF' -configopts += '-DENABLE_VTK=OFF' -configopts += '-DENABLE_CGAL=OFF' -configopts += '-DENABLE_PFVFLOW=OFF' - -# In case you want disable some Yade features -# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' - -# options available, -# ENABLE_GUI: enable GUI option (ON by default) -# ENABLE_CGAL: enable CGAL option (ON by default) -# ENABLE_VTK: enable VTK-export option (ON by default) -# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) -# ENABLE_GTS: enable GTS-option (ON by default) -# ENABLE_GL2PS: enable GL2PS-option (ON by default) -# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) -# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) -# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) -# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) -# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) -# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) -# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) -# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) -# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) -# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) -# USE_QT5: use QT5 for GUI, experimental (OFF by default) - -sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], - 'dirs': ['lib/x86_64-linux-gnu/yade-%(versio)s/py/yade'], -} - -moduleclass = 'devel' -- GitLab From 7c81af64d32804f56413cc5416b97fb2677def34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2016 23:49:31 +0200 Subject: [PATCH 0679/2403] modify easyconfig expat-2.1.1-intel-2016a.eb --- easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb index a442e3de7f..6e5b60c35f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-intel-2016a.eb @@ -10,7 +10,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCELOWER_TAR_BZ2] source_urls = [SOURCEFORGE_SOURCE] moduleclass = 'tools' -- GitLab From 122f7ad45fc9a1a435d6d64345cc2b05dbbf397e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:00:08 +0200 Subject: [PATCH 0680/2403] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb index d256bae534..4f86721ed0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -15,6 +15,7 @@ source_urls = [GNU_SOURCE] dependencies = [ ('libxml2', '2.9.3'), + ('ncurses', '6.0'), ] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' -- GitLab From 58f5d1437754085e98623da578ab3b58ad86bb29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:01:41 +0200 Subject: [PATCH 0681/2403] add missing ncurses dep + --with-libxml2-prefix to gettext easyconfigs --- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index b35aee8501..690872c686 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '5.9'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb index 168b2490e6..4580e48c6a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -18,6 +18,6 @@ dependencies = [ ('ncurses', '6.0'), ] -configopts = '--without-emacs' +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' -- GitLab From e069726a05c66e508bbf5651d5a5f935e2856f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 00:45:06 +0200 Subject: [PATCH 0682/2403] modify easyconfig GLib-2.48.0-intel-2016a.eb --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 6f5acf6419..d241317450 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,9 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +parallel = 1 postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] -- GitLab From 98217a3d259ea96af0512a3970fac83d2d6621d7 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 29 Apr 2016 21:11:40 -0400 Subject: [PATCH 0683/2403] add GL2PS-1.3.9_foss2016a-mesa11.2.1 --- .../c/CMake/CMake-3.5.2-foss-2016a.eb | 31 +++++++++ .../freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb | 40 +++++++++++ .../f/freetype/freetype-2.6.3-foss-2016a.eb | 22 ++++++ .../GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb | 37 ++++++++++ .../l/LLVM/LLVM-3.8.0-foss-2016a.eb | 41 +++++++++++ .../libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb | 27 ++++++++ ...ibXfont-1.5.1-foss-2016a-freetype-2.6.3.eb | 34 ++++++++++ .../l/libdrm/libdrm-2.4.68-foss-2016a.eb | 28 ++++++++ .../m/Mesa/Mesa-11.2.1-foss-2016a.eb | 68 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb | 21 ++++++ .../pkg-config-0.29.1-foss-2016a.eb | 27 ++++++++ 11 files changed, 376 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb new file mode 100644 index 0000000000..9075c094fb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..1965349120 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb new file mode 100644 index 0000000000..bc610c637e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..726a6db2a2 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb new file mode 100644 index 0000000000..fc0af540c1 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.0-foss-2016a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Python', '2.7.11'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..38c8310594 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('Mesa', mesa_ver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000..63d5bbf444 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-foss-2016a-freetype-2.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +freetype_ver = '2.6.3' +versionsuffix = '-freetype-%s' % freetype_ver + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3'), + ('freetype', freetype_ver), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.%s' % SHLIB_EXT, 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb new file mode 100644 index 0000000000..68f8a6be89 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb new file mode 100644 index 0000000000..a919f2eab9 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('glproto', '1.4.17'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.28'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libdrm', '2.4.68'), + ('libX11', '1.6.3',), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4'), + ('libXfont', '1.5.1', '-freetype-2.6.3'), + ('LLVM', '3.8.0'), + ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb new file mode 100644 index 0000000000..a5aab91ad9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1s' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb new file mode 100644 index 0000000000..bb2fea6cae --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8763ec11daf42708cb05942de98f37dc6f1547fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 30 Apr 2016 08:51:13 +0100 Subject: [PATCH 0684/2403] add easyconfig kallisto-0.42.5-foss-2016a.eb --- .../k/kallisto/kallisto-0.42.5-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb new file mode 100644 index 0000000000..2287c59cc6 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.42.5-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.42.5' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.4.3')] +dependencies = [('HDF5', '1.8.16', '-serial')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e9a1f252c40bda55d59d7f28cf83b4bbefed3088 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 10:19:47 +0200 Subject: [PATCH 0685/2403] no need to disable parallel building of GLib --- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index d241317450..918c5aec06 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -23,8 +23,6 @@ builddependencies = [('Python', '2.7.11')] configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" -parallel = 1 - postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { -- GitLab From ac03452b0d0306e26a04f301fa06be66aae5c288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2016 10:28:00 +0200 Subject: [PATCH 0686/2403] use check_conflicts function in easyconfigs tests --- test/easyconfigs/easyconfigs.py | 54 ++------------------------------- 1 file changed, 2 insertions(+), 52 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index db5060f0b6..a3f79cddc5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -54,7 +54,7 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool -from easybuild.tools.robot import resolve_dependencies +from easybuild.tools.robot import check_conflicts, resolve_dependencies from easybuild.tools.options import set_tmpdir @@ -145,57 +145,7 @@ class EasyConfigTest(TestCase): if self.ordered_specs is None: self.process_all_easyconfigs() - def mk_dep_mod_name(spec): - return tuple(EasyBuildMNS().det_full_module_name(spec).split(os.path.sep)) - - # construct a dictionary: (name, installver) tuple to (build) dependencies - depmap = {} - for spec in self.ordered_specs: - # exclude external modules, since we can't check conflicts on them (we don't even know the software name) - build_deps = [mk_dep_mod_name(d) for d in spec['builddependencies'] if not d.get('external_module', False)] - deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d.get('external_module', False)] - - # separate runtime deps from build deps - runtime_deps = [d for d in deps if d not in build_deps] - key = tuple(spec['full_mod_name'].split(os.path.sep)) - depmap.update({key: [build_deps, runtime_deps]}) - - # iteratively expand list of dependencies - depmap_last = None - while depmap != depmap_last: - depmap_last = copy.deepcopy(depmap) - for (spec, (build_deps, runtime_deps)) in depmap_last.items(): - # extend runtime dependencies with non-build dependencies of own runtime dependencies - for dep in runtime_deps: - depmap[spec][1].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][1] = sorted(nub(depmap[spec][1])) - # extend build dependencies with non-build dependencies of own build dependencies - for dep in build_deps: - depmap[spec][0].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][0] = sorted(nub(depmap[spec][0])) - - def check_conflict((name, installver), (name1, installver1), (name2, installver2)): - """Check whether dependencies with given name/(install) version conflict with each other.""" - # dependencies with the same name should have the exact same install version - # if not => CONFLICT! - if name1 == name2 and installver1 != installver2: - specname = '%s-%s' % (name, installver) - vs_msg = "%s-%s vs %s-%s" % (name1, installver1, name2, installver2) - print "Conflict found for dependencies of %s: %s" % (specname, vs_msg) - return True - else: - return False - - # for each of the easyconfigs, check whether the dependencies (incl. build deps) contain any conflicts - conflicts = False - for ((name, installver), (build_deps, runtime_deps)) in depmap.items(): - # also check whether module itself clashes with any of its dependencies - for i, dep1 in enumerate(build_deps + runtime_deps + [(name, installver)]): - for dep2 in (build_deps + runtime_deps)[i+1:]: - # don't worry about conflicts between module itself and any of its build deps - if dep1 != (name, installver) or dep2 not in build_deps: - conflicts |= check_conflict((name, installver), dep1, dep2) - self.assertFalse(conflicts, "No conflicts detected") + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool()), "No conflicts detected") def test_sanity_check_paths(self): """Make sure specified sanity check paths adher to the requirements.""" -- GitLab From a953b7c3339cf33506e33cdbaa31854adcc17ecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 30 Apr 2016 15:25:19 +0200 Subject: [PATCH 0687/2403] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 863911703e..3ab1f8aa60 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = [XORG_UTIL_SOURCE] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +builddependencies = [ + ('xproto', '7.0.28'), +] sanity_check_paths = { 'files': ['bin/makedepend'], -- GitLab From e169054960d7fe14c56efbe8ab31848b0834a460 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:15:18 +0100 Subject: [PATCH 0688/2403] add easyconfig SCons-2.4.1-foss-2016a-Python-2.7.11.eb --- .../SCons-2.4.1-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..35083b9098 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.4.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From aa31d54e3c255b37ae53239a86b93ae09956e6ec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 1 May 2016 00:17:18 +0100 Subject: [PATCH 0689/2403] add easyconfig Rosetta-2016.13.58602-foss-2016a.eb --- .../Rosetta-2016.13.58602-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb new file mode 100644 index 0000000000..86250d9275 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2016.13.58602-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '2016.13.58602' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.4.1', '-Python-2.7.11')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' -- GitLab From 6c0806d4dee7561c9a7465275e9be2dfdee26d7a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:37:57 +0200 Subject: [PATCH 0690/2403] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index 3ab1f8aa60..c9e59044e7 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] +source_urls = [XORG_UTIL_SOURCE] builddependencies = [ ('xproto', '7.0.28'), -- GitLab From f50236ed9bf05c28dfe03514332307491b0550a9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:39:37 +0200 Subject: [PATCH 0691/2403] modify easyconfig makedepend-1.0.5-foss-2016a.eb --- .../easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index c9e59044e7..c4a3658b9f 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -#source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] source_urls = [XORG_UTIL_SOURCE] builddependencies = [ -- GitLab From 1ceb9f59820d3cce159fb76b4c12175c99c2169b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:43:30 +0200 Subject: [PATCH 0692/2403] modify easyconfig Doxygen-1.8.11-foss-2016a.eb --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb index fea350b755..45e774b0e3 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From f05b80bccdb74af88f109105f8f5423d0f50f6c1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:47:00 +0200 Subject: [PATCH 0693/2403] modify easyconfig Perl-5.22.1-foss-2016a.eb --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index 404b98df7e..f1ad7853f0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 53c9b1c80a460c6543bbef815d616a396917d8fe Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 1 May 2016 12:57:16 +0200 Subject: [PATCH 0694/2403] add easyconfig PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb --- ...-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb new file mode 100644 index 0000000000..0d3d65891c --- /dev/null +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'PLplot' +version = '5.11.1' + +homepage = 'http://plplot.sourceforge.net' +description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols + and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +javaver = '1.7.0_79' +pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) + +glibver = '2.47.5' + +builddependencies = [ + ('CMake', '3.4.3'), + ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('xproto', '7.0.28'), +] + +dependencies = [ + ('Java', javaver, '', True), + ('Python', pyver), + ('Perl', '5.22.1'), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), + ('cairo', '1.14.6'), + ('expat', '2.1.0'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLib', glibver), + ('libICE', '1.0.9'), + ('libtool', '2.4.6'), + ('libX11', '1.6.3'), + ('libXau', '1.0.8'), + ('libxcb', '1.11.1'), + ('libXdmcp', '1.1.2'), + ('libXext', '1.3.3'), + ('libXrender', '0.9.9'), + ('Pango', '1.39.0'), + ('pixman', '0.34.0'), + ('zlib', '1.2.8') +] + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], + 'dirs': ['bin', 'include/plplot', 'lib/fortran/modules/plplot', 'lib/pkgconfig', 'share/man/man1'], +} + +moduleclass = 'vis' -- GitLab From 44b6590f2ca4b0683e2a2b922ebec71d555f0e25 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 15:50:56 +0200 Subject: [PATCH 0695/2403] builddep up --- .../easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 444de341bf..2facea57d9 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -19,12 +19,13 @@ sources = ['%(name)s_%(version)s.tgz'] dependencies = [('Boost', '1.60.0')] +builddependencies = [('CMake', '3.4.3',)] + + start_dir = 'src' configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST" -builddependencies = [('CMake', '3.4.3',)] - sanity_check_paths = { 'files': ['bin/CrossTalkZ'], 'dirs': [''], -- GitLab From d5f98a30a0c96ca87d29c8b47200cb2c4d6450a5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 16:08:28 +0200 Subject: [PATCH 0696/2403] version fix, commit version provided --- ....eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/Commet/{Commet-20160422-foss-2016a-Python-2.7.11.eb => Commet-20150415-foss-2016a-Python-2.7.11.eb} (76%) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb similarity index 76% rename from easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 2c16bccce7..88a548fab4 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20160422-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,8 @@ easyblock = 'MakeCp' name = 'Commet' -version = '20160422' +version = '20150415' +commit = '4ef0705' pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' @@ -13,11 +14,10 @@ a large metagenomic project. toolchain = {'name': 'foss', 'version': '2016a'} -# there is no tarball provided, only git checkout through: -# https://github.com/pierrepeterlongo/commet/archive/master.zip -sources = [SOURCE_ZIP] +source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] +sources = ['%s.tar.gz' % commit] -checksums = ['5fe63369ec3722e9e758b7bc1dcdfef3'] +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] -- GitLab From 540113e091905d193da3fcdc0c803424c34acd4a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 17:24:15 +0200 Subject: [PATCH 0697/2403] Exonerate with foss2016a --- .../e/Exonerate/Exonerate-2.4.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb new file mode 100644 index 0000000000..0cfe11f239 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/nathanweeks/exonerate/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GLib', '2.47.5')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' -- GitLab From 01bc3c39e0364364ea288d9e64c6adacf4533d63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2016 18:54:55 +0200 Subject: [PATCH 0698/2403] also add xproto as build dep in other makedepend 1.0.5 easyconfigs --- .../makedepend-1.0.5-gimkl-2.11.5.eb | 4 ++++ .../makedepend-1.0.5-intel-2015a.eb | 4 ++++ .../makedepend-1.0.5-intel-2015b.eb | 4 ++++ .../makedepend-1.0.5-intel-2016a.eb | 4 ++++ .../x/xproto/xproto-7.0.28-intel-2015a.eb | 24 +++++++++++++++++++ 5 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb index 38d76d37d2..29139d3313 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-gimkl-2.11.5.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb index 282179280a..2a137852f4 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb index ca6025105b..32cc5814c9 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015b.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index e38d07d26e..943da96f82 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -12,6 +12,10 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_UTIL_SOURCE] +builddependencies = [ + ('xproto', '7.0.28'), +] + sanity_check_paths = { 'files': ['bin/makedepend'], 'dirs': [], diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb new file mode 100644 index 0000000000..532a92d315 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.28' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 4a496d0696387804d39ae0782243921dcc9a5006 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 1 May 2016 21:45:01 +0200 Subject: [PATCH 0699/2403] Style fixes --- .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 88a548fab4..6c4d59ab68 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -3,13 +3,11 @@ easyblock = 'MakeCp' name = 'Commet' version = '20150415' commit = '4ef0705' - -pyver = '2.7.11' versionsuffix = '-Python-%(pyver)s' homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of -a large metagenomic project. + a large metagenomic project. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,15 +17,15 @@ sources = ['%s.tar.gz' % commit] checksums = ['19cba09ca7a92eaed75ed6af820d9451'] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] - dependencies = [ ('Python', '2.7.11'), ] +files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] + sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["Commet.py", "bvop", - "compare_reads", "extract_reads", "filter_reads", "index_and_search"]], + 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From 9e74175aa5e6096dcc34ad1f3a502b9a84dcfecc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:42:42 +0200 Subject: [PATCH 0700/2403] Add SWIG-3.0.8-foss-2016a-Python-2.7.11.eb --- .../SWIG-3.0.8-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2ffde034da --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.8' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.11' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From 7c7e981088c0df6a663f3ad8626980db936c01b3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 08:49:05 +0200 Subject: [PATCH 0701/2403] Modify Perl-5.22.1-intel-2016a.eb to update source_urls --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index aed8a467d0..b58ce50af4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -137,7 +137,7 @@ exts_list = [ }), ('FreezeThaw', '0.5001', { 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], }), ('DBI', '1.634', { 'source_tmpl': 'DBI-1.634.tar.gz', @@ -221,7 +221,7 @@ exts_list = [ }), ('Tie::Function', '0.02', { 'source_tmpl': 'Tie-Function-0.02.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', -- GitLab From 1d32aabaede918e266733560e3c7e573cd63b066 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 09:00:15 +0200 Subject: [PATCH 0702/2403] Modify Doxygen-1.8.11-* files to only build in serial --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb | 2 ++ easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb index 5adccf48d7..9af65e4593 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCC-4.9.2.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb index 1db648e43d..5b5d5f06cd 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2015a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb index 2d5dc8597f..a63ff80fea 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016a.eb @@ -16,4 +16,6 @@ builddependencies = [ ('Bison', '3.0.4'), ] +parallel = 1 + moduleclass = 'devel' -- GitLab From 752eeed94e82927ba6a1e12b2966bd95cd1a0342 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 10:07:56 +0200 Subject: [PATCH 0703/2403] bump Java to 1.7.0_80, use %(pyver)s, %(javaver)s templates --- ...-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/p/PLplot/{PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb => PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb} (77%) diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb similarity index 77% rename from easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index 0d3d65891c..a77bf58f49 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'PLplot' version = '5.11.1' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' homepage = 'http://plplot.sourceforge.net' description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols @@ -13,22 +14,15 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -pyver = '2.7.11' -javaver = '1.7.0_79' -pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-Java-%s-Python-%s' % (javaver, pyver) - -glibver = '2.47.5' - builddependencies = [ ('CMake', '3.4.3'), - ('SWIG', '3.0.8', '-foss-2016a-Python-%s' % pyver, True), + ('SWIG', '3.0.8', '-Python-%(pyver)s'), ('xproto', '7.0.28'), ] dependencies = [ - ('Java', javaver, '', True), - ('Python', pyver), + ('Java', '1.7.0_80', '', True), + ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), ('Tk', '8.6.4', '-no-X11'), @@ -36,7 +30,7 @@ dependencies = [ ('expat', '2.1.0'), ('fontconfig', '2.11.94'), ('freetype', '2.6.2'), - ('GLib', glibver), + ('GLib', '2.47.5'), ('libICE', '1.0.9'), ('libtool', '2.4.6'), ('libX11', '1.6.3'), @@ -52,7 +46,7 @@ dependencies = [ separate_build_dir = True -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], -- GitLab From 68da87ecb25dc92b328c3c313eaeb8192e6269d2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 2 May 2016 10:59:03 +0200 Subject: [PATCH 0704/2403] add easyconfig SPRNG-2.0b-foss-2016a.eb --- .../s/SPRNG/SPRNG-2.0b-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb new file mode 100644 index 0000000000..59be5269fa --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'SPRNG' +version = '2.0b' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.sprng.org/Version2.0/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = ['SPRNG-2.0_fix-metropolis-test.patch'] + +dependencies = [('GMP', '6.1.0')] + +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' + +# does not support parallel build +parallel = 1 + +files_to_copy = [ + (['lib/libsprng.a'], 'lib'), + (['include/interface.h', 'include/sprng.h', 'include/sprng_f.h'], 'include'), +] + +sanity_check_paths = { + 'files': ["lib/libsprng.a"], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From f12417d1caa6603e778b58af79d1235ad42d74db Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 2 May 2016 11:53:18 +0200 Subject: [PATCH 0705/2403] removed tab --- .../c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 6c4d59ab68..549296f08e 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', - 'extract_reads', 'filter_reads', 'index_and_search']], + 'extract_reads', 'filter_reads', 'index_and_search']], 'dirs' : ['doc', 'include'] } -- GitLab From d9ccb6471e949227ec1acd518aa95cf819737b81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 11:56:40 +0200 Subject: [PATCH 0706/2403] add easyconfig TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb, add easyconfig molmod-1.1-intel-2016a-Python-2.7.11.eb --- .../molmod-1.1-intel-2016a-Python-2.7.11.eb | 31 ++++++++++++++++++ .../TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1673c64e60 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..34a9b5e9f5 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.9-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.9' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), + ('molmod', '1.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' -- GitLab From 7e1df6e4e780696abbb408d269a01c77f473ee82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:10:49 +0200 Subject: [PATCH 0707/2403] add easyconfig FFmpeg-2.8.7-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb new file mode 100644 index 0000000000..05478ccada --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 56d851d169447389e2ee3cdfd4b04ef3e6f12a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 12:55:35 +0200 Subject: [PATCH 0708/2403] add easyconfig GTK+-2.24.30-intel-2016a.eb, add easyconfig Pango-1.40.1-intel-2016a.eb, add easyconfig cairo-1.14.6-intel-2016a-GLib-2.48.0.eb, add easyconfig HarfBuzz-1.2.7-intel-2016a.eb, add easyconfig ATK-2.20.0-intel-2016a.eb, add easyconfig Gdk-Pixbuf-2.35.1-intel-2016a.eb, add easyconfig GObject-Introspection-1.48.0-intel-2016a.eb --- .../a/ATK/ATK-2.20.0-intel-2016a.eb | 34 +++++++++++ .../cairo-1.14.6-intel-2016a-GLib-2.48.0.eb | 56 +++++++++++++++++++ ...Object-Introspection-1.48.0-intel-2016a.eb | 48 ++++++++++++++++ .../g/GTK+/GTK+-2.24.30-intel-2016a.eb | 25 +++++++++ .../Gdk-Pixbuf-2.35.1-intel-2016a.eb | 34 +++++++++++ .../h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 34 +++++++++++ .../p/Pango/Pango-1.40.1-intel-2016a.eb | 31 ++++++++++ 7 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb new file mode 100644 index 0000000000..2c8911864b --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..ecd56f9166 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb new file mode 100644 index 0000000000..3d59c6fe7c --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb new file mode 100644 index 0000000000..6dfeab0526 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb new file mode 100644 index 0000000000..f06da781d8 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb new file mode 100644 index 0000000000..23c2924fab --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb new file mode 100644 index 0000000000..b251f8ef22 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('HarfBuzz', '1.2.7'), + ('GObject-Introspection', '1.48.0'), + ('fontconfig', '2.11.95') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From b430a93dab623ccdbb1cbab087ef880ceac1942c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:12:56 +0200 Subject: [PATCH 0709/2403] add easyconfig NASM-2.12.01-intel-2016a.eb, add easyconfig x264-20160430-intel-2016a.eb --- .../n/NASM/NASM-2.12.01-intel-2016a.eb | 31 +++++++++++++++++++ .../x/x264/x264-20160430-intel-2016a.eb | 24 ++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb new file mode 100644 index 0000000000..dc884fc260 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb new file mode 100644 index 0000000000..2525aff2b3 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From a4e13eba05271a1af27d9e133bab189308dfe211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 13:48:06 +0200 Subject: [PATCH 0710/2403] modify easyconfig x264-20160430-intel-2016a.eb --- easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb index 2525aff2b3..5f7b69a6bc 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-intel-2016a.eb @@ -9,7 +9,10 @@ description = """x264 is a free software library and application for encoding vi toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['ftp://ftp.videolan.org/pub/videolan/x264/snapshots/'] +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] dependencies = [('Yasm', '1.3.0')] -- GitLab From e98a77f0534b917a23df6f63b4f7975391815725 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 15:09:25 +0200 Subject: [PATCH 0711/2403] add easyconfig OpenCV-2.4.12-intel-2016a.eb --- .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb new file mode 100644 index 0000000000..5cbe53aac8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.12' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +javaver = '1.7.0_80' +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('FFmpeg', '2.8.7'), + ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', javaver, '', True), + ('ant', '1.9.6', '-Java-%s' % javaver, True), + ('GLib', '2.48.0'), + ('GTK+', '2.24.30'), +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From 01c5819ff4a7441070afba2a3d05fc512b2e3e1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 16:37:32 +0200 Subject: [PATCH 0712/2403] use existing patch file, fix conflict on NASM version --- ...eg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb | 33 +++++++++++++++++++ .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 8 ++--- 2 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000..c1f7d100e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-intel-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 5cbe53aac8..89e2746bd8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -11,10 +11,10 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCELOWER_ZIP] -source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] -patches = ['OpenCV-%(version)s_with_IPP.patch'] +patches = ['OpenCV-2.4.9_with_IPP.patch'] builddependencies = [ ('CMake', '3.5.2'), @@ -25,7 +25,7 @@ dependencies = [ ('Python', '2.7.11'), ('zlib', '1.2.8'), ('FFmpeg', '2.8.7'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), -- GitLab From 1dc2cb9ea6258091ac20deafdd03dc35dfd23bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:05:52 +0200 Subject: [PATCH 0713/2403] add sed command to worker easyconfig files to fix module_path in conf/worker.conf --- .../easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 9 +++++---- .../easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index cdf0174497..66e66633d0 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2015a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index 3c373e597a..f840fe2253 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -21,11 +21,12 @@ dependencies = [ # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ - 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) - 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From 674a21915757f47ee9b7847046f3342ea1c5f39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:26:36 +0200 Subject: [PATCH 0714/2403] add easyconfig FFTW-3.3.4-intel-2016a.eb --- .../f/FFTW/FFTW-3.3.4-intel-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb new file mode 100644 index 0000000000..09d52dd755 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 9c81999977bfae80711d38da02ebd8912caa5468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 17:32:59 +0200 Subject: [PATCH 0715/2403] make Gdk-Pixbug 2.35.1 compatible with NASM 2.12.01 --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb index f06da781d8..ec51681b28 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GLib', '2.48.0'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('GObject-Introspection', '1.48.0') -- GitLab From 0933f2c4ce3c791af9049d58a213777de638df6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:13:57 +0200 Subject: [PATCH 0716/2403] correct sed command in worker easyconfig files to fix module_path in conf/worker.conf --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index 66e66633d0..1bd2831171 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb index f840fe2253..1882b094dc 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.4-intel-2016a.eb @@ -26,7 +26,7 @@ postinstallcmds = [ 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016a@g" %(installdir)s/conf/worker.conf', - 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../modules/all@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] moduleclass = 'tools' -- GitLab From dcd16bf4a00f49d8511d31f894606d306cb5b08e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2016 19:47:01 +0200 Subject: [PATCH 0717/2403] bump hwloc to 1.11.3, add missing hwloc easyconfig file --- .../hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 22 +++++++++++++++++++ .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..54ea46766a --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +# numactl is a direct dependency of PGI +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 8cd6dea646..be813ed50e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify -dependencies = [('hwloc', '1.11.2')] +dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -- GitLab From ced0e99cf03255aa46d0855c8ee42cfe2e691835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:18:33 +0200 Subject: [PATCH 0718/2403] add easyconfig ParaView-4.4.0-intel-2016a.eb --- .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb new file mode 100644 index 0000000000..5961519cd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': False} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('Mesa', '11.2.1'), + ('libGLU', '9.0.0'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +maxparallel = 4 + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +# Without internet connection turn off testing (uncomment the following line) +#configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From bb3540dfc10e41c0550bb4aa18610f15e8be76f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:23:40 +0200 Subject: [PATCH 0719/2403] modify easyconfig ParaView-4.4.0-intel-2016a.eb, add easyconfig libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb --- .../libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb | 27 +++++++++++++++++++ .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 3 +-- 2 files changed, 28 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fe3cfb14d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index 5961519cd4..dd7ed0db4e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -16,8 +16,7 @@ sources = ["ParaView-v%(version)s-source.tar.gz"] patches = ['%(name)s-%(version)s_missingheader.patch'] dependencies = [ - ('Mesa', '11.2.1'), - ('libGLU', '9.0.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libXt', '1.1.5'), ('Qt', '4.8.7'), ('libXext', '1.3.3'), -- GitLab From bdcebe8ebd643eedf64753a77bdb8a0500edf040 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:29:46 +0200 Subject: [PATCH 0720/2403] DIAL with foss2016a --- .../d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb new file mode 100644 index 0000000000..9698cc436f --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'DIAL' +version = '2011.06.06' + +homepage = 'http://www.bx.psu.edu/miller_lab/' +description = """ +DIAL (De novo Identification of Alleles) is a collection of programs to automate +the discovery of alleles for a species where we lack a reference sequence. The +SNPs/alleles are specifically selected for a low error rate in genotyping +assays. +""" + + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['DIAL-Makefile.in.patch'] + +dependencies = [ + ('LASTZ', '1.02.00'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in [ + 'assemble', + 'assemble1', + 'assemble_illumina', + 'build_sff_index', + 'convertFastqFasta', + 'cull_components', + 'DIAL', + 'filter', + 'filter_clusters', + 'fish_clusters', + 'make_template', + 'masker', + 'partition', + 'remove_clones', + 'remove_clusters', + 'update', + 'update_clusters', + 'update_status', +]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From 4d95db4024048043a88926c1ab85b70103c54b1b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:38:51 +0200 Subject: [PATCH 0721/2403] LASTZ with foss2016a --- .../l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb new file mode 100644 index 0000000000..6f1e587143 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['LASTZ-Makefile.patch'] + +skipsteps=['configure'] + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From 86534840b088b9961b865fe76a0494db0932d37d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:46:53 +0200 Subject: [PATCH 0722/2403] longlines --- .../easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 9698cc436f..3f508bfac5 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -4,14 +4,11 @@ name = 'DIAL' version = '2011.06.06' homepage = 'http://www.bx.psu.edu/miller_lab/' -description = """ -DIAL (De novo Identification of Alleles) is a collection of programs to automate -the discovery of alleles for a species where we lack a reference sequence. The -SNPs/alleles are specifically selected for a low error rate in genotyping -assays. +description = """DIAL (De novo Identification of Alleles) is a collection of programs + to automate the discovery of alleles for a species where we lack a reference sequence. + The SNPs/alleles are specifically selected for a low error rate in genotyping assays. """ - toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] -- GitLab From bd6a68f0019b2a28271c533b904a43dea7518149 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:50:20 +0200 Subject: [PATCH 0723/2403] disable testing for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index dd7ed0db4e..e9e923fc24 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -34,7 +34,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) -- GitLab From a5acebaa141c7adea90c1ebc41016336c2c231bd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 3 May 2016 11:53:50 +0200 Subject: [PATCH 0724/2403] comments exts --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 1e9c0c19f5..fdb264f023 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -18,12 +18,13 @@ dependencies = [ ('DB_File', '1.835', versionsuffix), ] -exts_list = [ - ('CGI', '4.28', { - 'source_tmpl': 'CGI-4.28.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], - }), -] +#exts_list = [ +# ('CGI', '4.28', { +# 'source_tmpl': 'CGI-4.28.tar.gz', +# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], +# }), +#] + options = {'modulename': 'Bio::Perl'} moduleclass = 'bio' -- GitLab From 9b8e5bb3f71195e5ada26a6ebfa928b8772a03f7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 3 May 2016 11:55:27 +0200 Subject: [PATCH 0725/2403] modify easyconfig Blitz++-0.10-foss-2016a.eb, modify easyconfig Blitz++-0.10-goolf-1.5.16.eb --- easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb | 2 ++ easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb index f91bad5dd3..f5aaed761c 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-foss-2016a.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb index f75014e6f2..e75ab2de98 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-goolf-1.5.16.eb @@ -17,4 +17,6 @@ sanity_check_paths = { 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', 'include/random', 'lib/pkgconfig'], } +configopts = '--enable-shared' + moduleclass = 'lib' -- GitLab From 9d63140391fe52ab6161f2df09171600fa04a875 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 11:57:35 +0200 Subject: [PATCH 0726/2403] add easyconfig grace-5.1.25-intel-2016a.eb, add easyconfig util-linux-2.28-intel-2016a.eb, add easyconfig motif-2.3.5-intel-2016a.eb, add easyconfig xbitmaps-1.1.1-intel-2016a.eb --- .../g/grace/grace-5.1.25-intel-2016a.eb | 29 ++++++++++++ .../m/motif/motif-2.3.5-intel-2016a.eb | 47 +++++++++++++++++++ .../util-linux/util-linux-2.28-intel-2016a.eb | 33 +++++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb | 19 ++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb new file mode 100644 index 0000000000..e538b0ca3b --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000..ed700e2d0b --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.5' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXau', '1.0.8'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.21'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.6.3'), + ('libjpeg-turbo', '1.4.2'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('util-linux', '2.28'), +] + +preconfigopts = "./autogen.sh && " + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb new file mode 100644 index 0000000000..d86cc6a029 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.28' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb new file mode 100644 index 0000000000..a463f1ce79 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From f574411b83f9fda2f0dda5862b40ae1996aaa6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:04:35 +0200 Subject: [PATCH 0727/2403] fix source URL for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index ed700e2d0b..60a8ac80b7 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s-src.tgz'] +sources = ['%(name)s-%(version)s.tgz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 16f0c91739daa1cdf1cd19d283b29ae22a246d3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:09:34 +0200 Subject: [PATCH 0728/2403] really fix name of source tarball for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 60a8ac80b7..8072aeb7c2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # use -O1 to dance around icc segfaulting toolchainopts = {'lowopt': True} -sources = ['%(name)s-%(version)s.tgz'] +sources = ['%(name)s-%(version)s.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ -- GitLab From 025a13b46c76146c6ddcb0c82b80b741c34e09e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 12:18:58 +0200 Subject: [PATCH 0729/2403] no autogen for motif 2.3.5 --- easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb index 8072aeb7c2..0cf658c9a2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-intel-2016a.eb @@ -34,8 +34,6 @@ builddependencies = [ ('util-linux', '2.28'), ] -preconfigopts = "./autogen.sh && " - # makefile is not parallel safe parallel = 1 -- GitLab From 17fed7291663dfab3144c3c71acbfa5461e73a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2016 13:39:08 +0200 Subject: [PATCH 0730/2403] no need to limit parallel build for ParaView --- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index e9e923fc24..838808a743 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -28,8 +28,6 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -maxparallel = 4 - configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -- GitLab From 4ef76e210cf81d007716d81489e3e951d67589eb Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 4 May 2016 13:34:30 +0200 Subject: [PATCH 0731/2403] Easyconfig for Gurobi 6.5.1 --- .../easyconfigs/g/Gurobi/Gurobi-6.5.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb new file mode 100644 index 0000000000..4d3f74327c --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '6.5.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +# Registration is required. +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", name, "%(namelower)s.lic") + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in ['grbprobe', 'grbtune', 'gurobi_cl', 'gurobi.sh']], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 53289060c2f14243de149b5e4146de0924c5427e Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 4 May 2016 13:36:14 +0200 Subject: [PATCH 0732/2403] Easyconfig for Gurobi 6.5.1 --- .../easyconfigs/g/Gurobi/Gurobi-6.5.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb new file mode 100644 index 0000000000..4d3f74327c --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '6.5.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +# Registration is required. +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] + +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", name, "%(namelower)s.lic") + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in ['grbprobe', 'grbtune', 'gurobi_cl', 'gurobi.sh']], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 596390a3f4ace66c6329792d3e3849d2d45dc4c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 13:42:09 +0200 Subject: [PATCH 0733/2403] clean up binutils 2.26 easyconfigs to use binutils easyblock --- .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 20 ------------------- .../easyconfigs/b/binutils/binutils-2.26.eb | 20 ------------------- 2 files changed, 40 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index ca71c5f04e..d7c829040f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -20,22 +18,4 @@ builddependencies = [ ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index 5145e1becd..702b413120 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.26' @@ -18,22 +16,4 @@ builddependencies = [ ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 8580725e82c0690321e07d4588b0dfdac13968e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2016 14:30:10 +0200 Subject: [PATCH 0734/2403] clean up binutils easyconfigs to use binutils easyblock --- .../binutils-2.22-goalf-1.1.0-no-OFED.eb | 14 ----------- .../binutils-2.22-gompi-1.4.12-no-OFED.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.4.10.eb | 14 ----------- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 11 --------- .../b/binutils/binutils-2.24-foss-2014b.eb | 13 ----------- .../b/binutils/binutils-2.24-intel-2014b.eb | 16 ------------- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 23 +------------------ .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 23 +------------------ .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 22 +----------------- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.1.eb | 22 +----------------- .../easyconfigs/b/binutils/binutils-2.25.eb | 22 +----------------- 15 files changed, 9 insertions(+), 273 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index bfc339020f..af12b0472e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 437f04c2a6..8035182b62 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,15 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 5f76d89a06..de87300f7c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -23,15 +20,4 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 5dae8ebe27..d989a00acf 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -9,9 +9,6 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## - -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.22' @@ -24,12 +21,4 @@ toolchainopts = {'pic': True} sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 3d49fdcf03..9683cfc728 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,15 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 77fb03962b..5d4b31cd73 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.24' @@ -15,18 +13,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - -# disable warning/error #175 ("subscript out of range") -buildopts = 'CFLAGS="$CFLAGS -wd175"' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index c3ffc6e24a..08e10d150c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 418f81f5f1..ea9a13974b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 2e680c9ce3..9709696cf5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index b6d6a68fc6..7ccace8501 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -11,30 +9,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -# zlib required, but being linked instatically, so not a runtime dep builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 6858b124b1..d6e68008e5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -14,28 +12,10 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index a9d4815d89..9ec7a3f3f3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 5378940837..f411442d12 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,28 +13,10 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -# statically link with zlib, to avoid runtime dependency on zlib -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' -prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"' - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins --enable-shared --enable-static' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + - ['lib/lib%s.%s' % (l, x) for l in ['bfd', 'opcodes'] for x in ['a', SHLIB_EXT]] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index 63837a712c..e3f5b15724 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25.1' @@ -14,26 +12,8 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index cfcfe38d3d..e08cd975ad 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'binutils' version = '2.25' @@ -15,26 +13,8 @@ builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -# statically link with zlib, to avoid runtime dependency on zlib -# further, add the system library path in the rpath: this should 'harden' the -# resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc) -preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"' -prebuildopts = preconfigopts - -# make sure that system libraries are also considered by ld and ld.gold is also built -# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' - -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + - ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From 60b7998227658378f64bdb37d17b2d93cec9954f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 14:35:38 +0200 Subject: [PATCH 0735/2403] Add libcroco --- .../l/libcroco/libcroco-0.6.11-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb new file mode 100644 index 0000000000..29421c21ae --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.11-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.11' + +homepage = 'https://github.com/GNOME/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libcroco/%(version_major_minor)s/'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), + ('GLib', '2.48.0'), + ('XZ', '5.2.2',) +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' -- GitLab From 2b14bc7845376a3291b1a6ee367fde0cc6c866b1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 14:36:11 +0200 Subject: [PATCH 0736/2403] Build shared FLTK and enable threads --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index 97b3b63c16..226d6e353c 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -17,6 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ ('libX11', '1.6.3'), -- GitLab From f352cd263e6d396f3ee55d090ac2369d6f2fd1fe Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:01:57 +0200 Subject: [PATCH 0737/2403] Add librsvg --- .../l/librsvg/librsvg-2.40.15-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb new file mode 100644 index 0000000000..40a5c468bc --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.40.15' + +homepage = 'https://wiki.gnome.org/action/show/Projects/LibRsvg' +description = """librsvg is a library to render SVG files using cairo.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] + +dependencies = [ + ('Gdk-Pixbuf', '2.35.1'), + ('libcroco', '0.6.11'), + ('Pango', '1.40.1'), + ('cairo', '1.14.6', '-GLib-2.48.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'vis' -- GitLab From f5eb0bd2eaab60cf310f854add0143cd6c07a47d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:17:34 +0200 Subject: [PATCH 0738/2403] Make gettext build dep for XZ --- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index b717af018a..0d274e829e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -13,9 +13,6 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ ('gettext', '0.19.6'), ] -- GitLab From 6b794ab6f8552861afc6edb28e210a5ff3730a6c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:18:10 +0200 Subject: [PATCH 0739/2403] Add jwm --- .../j/jwm/jwm-2.3.5-intel-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb diff --git a/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb new file mode 100644 index 0000000000..46a293738e --- /dev/null +++ b/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'JWM' +version = '2.3.5' + +homepage = 'https://joewing.net/projects/jwm/' +description = """JWM is a light-weight window manager for the X11 Window System.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['https://joewing.net/projects/jwm/releases'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libX11', '1.6.3'), + ('libXft', '2.3.2'), + ('libXext', '1.3.3'), + ('libXmu', '1.1.2'), + ('libXpm', '3.5.11'), + ('libpng', '1.6.21'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libXinerama', '1.1.3'), + ('fontconfig', '2.11.95'), + ('cairo', '1.14.6', '-GLib-2.48.0'), + ('libcroco', '0.6.11'), + ('librsvg', '2.40.15'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'vis' -- GitLab From fb1473a41cc0fca45c09153b1c533a6ee4e07bec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:30:37 +0200 Subject: [PATCH 0740/2403] Capitalize jwm --- .../jwm-2.3.5-intel-2016a.eb => JWM/JWM-2.3.5-intel-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/j/{jwm/jwm-2.3.5-intel-2016a.eb => JWM/JWM-2.3.5-intel-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/j/jwm/jwm-2.3.5-intel-2016a.eb rename to easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb -- GitLab From 263190c2ecf45306f893665fd7a294b2f38dd75e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:37:57 +0200 Subject: [PATCH 0741/2403] Fix version hell --- .../j/JWM/JWM-2.3.5-intel-2016a.eb | 2 +- ...ft-2.3.2-intel-2016a-fontconfig-2.11.95.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb diff --git a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb index 46a293738e..273e8bedca 100644 --- a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb @@ -14,7 +14,7 @@ source_urls = ['https://joewing.net/projects/jwm/releases'] dependencies = [ ('bzip2', '1.0.6'), ('libX11', '1.6.3'), - ('libXft', '2.3.2'), + ('libXft', '2.3.2', '-fontconfig-2.11.95'), ('libXext', '1.3.3'), ('libXmu', '1.1.2'), ('libXpm', '3.5.11'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb new file mode 100644 index 0000000000..3c4a378321 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' +versionsuffix = '-fontconfig-2.11.95' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.3'), + ('fontconfig', '2.11.95'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From db94502b667bd318e0cd9b8124dc2cfa2d99ea2c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:49:56 +0200 Subject: [PATCH 0742/2403] Add sanity check --- easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb index 273e8bedca..754b3694f8 100644 --- a/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/j/JWM/JWM-2.3.5-intel-2016a.eb @@ -28,8 +28,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/jwm'], + 'dirs': ['etc', 'share'] } moduleclass = 'vis' -- GitLab From aa75dc672a73af64ccbbafe19281c4f415772167 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 15:51:20 +0200 Subject: [PATCH 0743/2403] FLTK: check of static and dynamic lib --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index 226d6e353c..e045fbcd6c 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid'], + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'libfltk.%s' % SHLIB_EXT], 'dirs': ['lib'], } -- GitLab From 78b5bbd0f7434449c304db593d6fa3c09a7ef9ab Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:00:37 +0200 Subject: [PATCH 0744/2403] Don't do GDK-pixbuf loader --- easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb index 40a5c468bc..9d059ba80c 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_XZ] source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] +# this loader wants to install in the directory of Gdk-Pixbuf itself, so disable +configopts = '--disable-pixbuf-loader' + dependencies = [ ('Gdk-Pixbuf', '2.35.1'), ('libcroco', '0.6.11'), -- GitLab From 053e882d140f2227a4fb0da572fcce5014e80f7a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:11:17 +0200 Subject: [PATCH 0745/2403] Add sanity check --- .../easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb index 9d059ba80c..57726fc9cd 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.40.15-intel-2016a.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/rsvg-convert', 'lib/librsvg-2.%s' % SHLIB_EXT, 'lib/librsvg-2.a'], + 'dirs': ['include/librsvg-2.0', 'share'] } moduleclass = 'vis' -- GitLab From 4f1e5b15a584305b53e92d193616e9a4f954cb2b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 May 2016 16:44:35 +0200 Subject: [PATCH 0746/2403] Fix sanity check --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index e045fbcd6c..859d8f39a4 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'libfltk.%s' % SHLIB_EXT], + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], 'dirs': ['lib'], } -- GitLab From 52e2b45e866b5d6c1c3779d6f19ebba6a3c12aa8 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 10:55:13 -0400 Subject: [PATCH 0747/2403] bump to GLib 2.48.0 --- .../g/GLib/GLib-2.48.0-foss-2016a.eb | 33 +++++++++++++++++++ .../PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb new file mode 100644 index 0000000000..73ce1be6d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.7'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), +] + +builddependencies = [('Python', '2.7.11')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index 9d7551949d..1438b0e86a 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ('GTS' ,'0.7.6'), ] -- GitLab From 61d8f74df864995f4a49d53ef64d108cd9ddf585 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:14:12 -0400 Subject: [PATCH 0748/2403] bump to mesa 11.2.1 --- ...bQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3f7a781e6b --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-foss-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' -- GitLab From 16181d207a81520c7b3d0b80143f37fb9a9e181f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:23:58 -0400 Subject: [PATCH 0749/2403] add Qt 4.8.7 with GLib-2.48.0 --- .../q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..8616257c5c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,27 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +glib_ver = '2.48.0' +versionsuffix = '-GLib-%s' % glib_ver + +dependencies = [ + ('GLib', glib_ver), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' -- GitLab From c3b8ffb5250bcdba45838b4b54b402414f6d9697 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 5 May 2016 11:53:26 -0400 Subject: [PATCH 0750/2403] bump to GLib 2.48.0 --- easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb index 6e89234d6b..cca1bedcdd 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2016a.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('GLib', '2.47.5'), + ('GLib', '2.48.0'), ] sanity_check_paths = { -- GitLab From 7e2777ca5529688af1eaf9595934fe727ca1b05d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 12:29:11 +0200 Subject: [PATCH 0751/2403] quickfixes --- .../d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 29 +++++-------------- 1 file changed, 7 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 3f508bfac5..a4838ae3d0 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -14,34 +14,19 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['DIAL-Makefile.in.patch'] +patches = ['DIAL-%(version)s_Makefile.in.patch'] dependencies = [ ('LASTZ', '1.02.00'), ] +binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', + 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', + 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', + 'update_status',] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in [ - 'assemble', - 'assemble1', - 'assemble_illumina', - 'build_sff_index', - 'convertFastqFasta', - 'cull_components', - 'DIAL', - 'filter', - 'filter_clusters', - 'fish_clusters', - 'make_template', - 'masker', - 'partition', - 'remove_clones', - 'remove_clusters', - 'update', - 'update_clusters', - 'update_status', -]], - 'dirs': ["bin"] + 'files': ['bin/%s' % bin for binfile in binaries], + 'dirs': ['bin'] } moduleclass = 'bio' -- GitLab From 8fc70c4034eaa8b0c805a15fa4cd50daf5fafa8e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:17:17 +0200 Subject: [PATCH 0752/2403] provided patch --- .../easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- .../easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 6f1e587143..e032219f9e 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-Makefile.patch'] +patches = ['LASTZ-1.02.00_Makefile.patch'] skipsteps=['configure'] diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch new file mode 100644 index 0000000000..e0aa55dbeb --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -0,0 +1,12 @@ +--- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 ++++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 +@@ -28,7 +28,7 @@ + # + #--------- + +-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE ++definedForAll = -Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE + + + VERSION_FLAGS= \ + -- GitLab From a2668ad34eeac9de4a4f5cb2e78272e9dd042329 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:20:41 +0200 Subject: [PATCH 0753/2403] quickfixes --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index e032219f9e..76b32edded 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -16,12 +16,12 @@ source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] patches = ['LASTZ-1.02.00_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] installopts = 'installDir=%(installdir)s/bin' sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["lastz","lastz_D"]], + 'files': ["bin/%s" % binfile for binfile in ["lastz", "lastz_D"]], 'dirs': ["bin"] } -- GitLab From 1930b858c49360948b786786cbb6aeffc4e17d96 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:47:49 +0200 Subject: [PATCH 0754/2403] FFmpeg with foss2016a --- .../f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb new file mode 100644 index 0000000000..b93565bb4f --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '2.8.7' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), + ('x264', '20160114'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From a29a5c6c3bbe98becf368f5dff527ddf07b413e4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 6 May 2016 13:51:38 +0200 Subject: [PATCH 0755/2403] FIAT with foss2016a --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..649eb41225 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order +instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +pyver = '2.7.11' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('sympy', '0.7.6.1', versionsuffix), +] + +options = {'modulename': name} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'math' -- GitLab From 14050d83c1b95894071cb5da2fb4ea2ec1da3158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 14:24:43 +0200 Subject: [PATCH 0756/2403] disable necessary buildopts for binutils 2.24 w/ intel/2014b --- easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 5d4b31cd73..7598e76c07 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -13,4 +13,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# disable warning/error #175 ("subscript out of range") +buildopts = 'CFLAGS="$CFLAGS -wd175"' + moduleclass = 'tools' -- GitLab From 8292a831911188e5673f608d0de9abc0c81a4ca2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 May 2016 21:12:59 +0200 Subject: [PATCH 0757/2403] {toolchain}[dummy] intel/2016.03-GCC-5.3 --- .../h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 18 ++++++++++ .../i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 18 ++++++++++ .../ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb | 20 +++++++++++ ...11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 36 +++++++++++++++++++ ....181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 33 +++++++++++++++++ .../i/intel/intel-2016.03-GCC-5.3.eb | 26 ++++++++++++++ 8 files changed, 217 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..7eaca67c16 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d81ed4bdf9 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] + +checksums = ['d6f8529a44231e427219c8e025dec3b2'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..a1f40c75ae --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2016.3.210' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..703424d3e0 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2016.3.210' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] + +checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..8e5a35ceef --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016.03' +versionsuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..82e5a9af1a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['536dbd82896d6facc16de8f961d17d65'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..cc0d58235f --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb new file mode 100644 index 0000000000..3de185ca63 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.3' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' -- GitLab From 892391bd9820632cb41dd723b2d9a46ae8ec6462 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 7 May 2016 23:46:07 +0100 Subject: [PATCH 0758/2403] Initial version of annovar for foss-2016a --- ...nnovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..af32067597 --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'annovar' +version = '2016Feb01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ ANNOVAR is an efficient software tool to utilize update-to-date information + to functionally annotate genetic variants detected from diverse genomes (including human + genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +sources = ['%(name)s.latest.tar.gz'] + +dependencies = [('Perl', '5.22.1')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +moduleclass = 'bio' -- GitLab From 64b203ccd0ade8375d5f1a698ec9b07adb88ae9c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 7 May 2016 23:48:44 +0100 Subject: [PATCH 0759/2403] add easyconfig annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb --- ...nnovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..af32067597 --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'annovar' +version = '2016Feb01' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ ANNOVAR is an efficient software tool to utilize update-to-date information + to functionally annotate genetic variants detected from diverse genomes (including human + genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# Registration required for download +# http://www.openbioinformatics.org/annovar/annovar_download_form.php +sources = ['%(name)s.latest.tar.gz'] + +dependencies = [('Perl', '5.22.1')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +moduleclass = 'bio' -- GitLab From 09b4e9468c5dd27612574fa2da9448e66dd37a2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 May 2016 07:29:48 +0200 Subject: [PATCH 0760/2403] fix checksums for icc/ifort 2016.3 and imkl 11.3.3 --- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index d81ed4bdf9..2192bcc506 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] -checksums = ['d6f8529a44231e427219c8e025dec3b2'] +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 703424d3e0..b354753609 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] -checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] gccver = '5.3.0' binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 82e5a9af1a..09806746b2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' -- GitLab From e1d1dbbfa433cf1e5c52482d274fba80c8219468 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 09:22:01 +0200 Subject: [PATCH 0761/2403] {toolchain}[dummy] foss/2016.04 --- .../f/FFTW/FFTW-3.3.4-gompi-2016.04.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2016.04.eb | 35 +++++++++++++ .../easyconfigs/g/gompi/gompi-2016.04.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 18 +++++++ .../h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb | 23 +++++++++ .../numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb | 23 +++++++++ ...BLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 51 +++++++++++++++++++ .../OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb | 32 ++++++++++++ ...pi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb | 25 +++++++++ 9 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2016.04.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016.04.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb new file mode 100644 index 0000000000..aeee54992e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.04.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.04.eb b/easybuild/easyconfigs/f/foss/foss-2016.04.eb new file mode 100644 index 0000000000..b70b879a23 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.04.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb new file mode 100644 index 0000000000..b978fd902a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.04' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.3.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.3.0 and binutils 2.26 + ('OpenMPI', '1.10.2', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb new file mode 100644 index 0000000000..e65fa73eda --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..5a122dc923 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..d7d6d78efa --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.3.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..d8f2e33a19 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..4502f5c9f4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..326e2d8f43 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2016.04'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '5.3.0-2.26'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From d70cc438be3667d0aed78dc8ac353bbae6a3ad2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 11:15:21 +0200 Subject: [PATCH 0762/2403] modify easyconfig Mathematica-10.4.1.eb --- .../m/Mathematica/Mathematica-10.4.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb new file mode 100644 index 0000000000..9d13deaf53 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.4.1' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From 176ad0202e8ea0ec6bff115ce32aa1cbe5449d77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 12:59:05 +0200 Subject: [PATCH 0763/2403] add easyconfig FLANN-1.8.4-intel-2016a-Python-2.7.11.eb --- .../FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..2072207364 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cs.ubc.ca/research/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.ubc.ca/research/flann/uploads/FLANN/'] +sources = ['flann-%(version)s-src.zip'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Python', '2.7.11'), +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = '' -- GitLab From a85f8ccc6a4f2eec679db0cbb58d270c32f0d0c0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 13:50:48 +0200 Subject: [PATCH 0764/2403] rm FIAT config --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 649eb41225..0000000000 --- a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'FIAT' -version = '1.6.0' - -homepage = 'https://bitbucket.org/fenics-project/fiat' -description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order -instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating -arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] -sources = [SOURCELOWER_TAR_GZ] - -pyver = '2.7.11' -versionsuffix = '-Python-%s' % pyver - -dependencies = [ - ('Python', pyver), - ('sympy', '0.7.6.1', versionsuffix), -] - -options = {'modulename': name} - -pyshortver = '.'.join(pyver.split('.')[:2]) -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'math' -- GitLab From b34ef4de8733009684425ad8f39f0480f561a19e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:21:45 +0200 Subject: [PATCH 0765/2403] updated NASM and x264 --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb index b93565bb4f..0badebf4eb 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -12,9 +12,9 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.11.08'), + ('NASM', '2.12.01'), ('zlib', '1.2.8'), - ('x264', '20160114'), + ('x264', '20160430'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From a88a6c7339fc37a4c19a29f58dc1ca32654d8383 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:24:38 +0200 Subject: [PATCH 0766/2403] NASM with foss 2016a --- .../n/NASM/NASM-2.12.01-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb new file mode 100644 index 0000000000..3097f4cb0e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.01' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 0839e877fbd375b3c22f3901ed9e7870346343f4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:27:02 +0200 Subject: [PATCH 0767/2403] x264 with foss2016a --- .../x/x264/x264-20160430-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb new file mode 100644 index 0000000000..5f7b69a6bc --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160430' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 5fb8dea52cb48755a96ff45156087c5071e3fcf5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:28:15 +0200 Subject: [PATCH 0768/2403] for foss --- easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb index 5f7b69a6bc..7a55229c71 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160430-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.videolan.org/developers/x264.html' description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://download.videolan.org/pub/videolan/x264/snapshots/', -- GitLab From 8caf1e4defeaff863d5b7205f6b1576e6837d914 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:31:35 +0200 Subject: [PATCH 0769/2403] FLASH with foss 2016a --- .../f/FLASH/FLASH-1.2.11-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb new file mode 100644 index 0000000000..5212c8b658 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '1.2.11' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software + tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to + merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. + The resulting longer reads can significantly improve genome assemblies. They can also improve + transcriptome assembly when FLASH is used to merge RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://download.sourceforge.net/%(namelower)spage'] +sources = [SOURCE_TAR_GZ] + +files_to_copy = [(['flash'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 486cc49fa3b8fda9c1a1d48d581e5decbe837fb8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 14:50:56 +0200 Subject: [PATCH 0770/2403] Yasm with foss 2016a --- .../y/Yasm/Yasm-1.3.0-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb new file mode 100644 index 0000000000..fd9ab5e210 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From cc7240533ac882ca7bfc16fffa56d51c6fa4365d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 15:19:19 +0200 Subject: [PATCH 0771/2403] provided author and explaination for patch --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch index e0aa55dbeb..39bfb5c655 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00_Makefile.patch @@ -1,3 +1,6 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) --- lastz-distrib-1.02.00/src/Makefile 2010-01-13 18:00:09.000000000 +0100 +++ lastz-distrib-1.02.00/src/Makefile 2015-02-09 17:22:41.030256461 +0100 @@ -28,7 +28,7 @@ -- GitLab From dac87e7edf7d9008f3446ec222660d8d80a6963d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 15:33:42 +0200 Subject: [PATCH 0772/2403] gensim with foss2016a --- .../gensim-0.12.4-foss-2016a-Python-2.7.11.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..4c0e09b879 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.12.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'lib' -- GitLab From 2e74be2bf1817e6e33b78b68b394223cde42a32b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:07:40 +0200 Subject: [PATCH 0773/2403] add easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, add easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb, add easyconfig Eigen-3.2.8-intel-2016a.eb --- .../e/Eigen/Eigen-3.2.8-intel-2016a.eb | 14 +++++ .../PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 33 ++++++++++ .../VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 60 +++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb new file mode 100644 index 0000000000..ec8373b9eb --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.8' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6c685288a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'PCL' +version = '1.7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://pointclouds.org/' +description = """The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and + point cloud processing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.8'), + ('FLANN', '1.8.4', versionsuffix), + ('VTK', '6.3.0', versionsuffix), + ('Qhull', '2015.2'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1302e71e57 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,60 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.5.2')] + +mesaver = '11.0.8' +dependencies = [ + ('Python', '2.7.11'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From da8956afd380f0e489f882180c6efea70d2d3955 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:23:20 +0200 Subject: [PATCH 0774/2403] drop toolchainopts from Eigen easyconfigs, since it is headers-only --- easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb | 1 - .../easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb | 1 - easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb | 1 - 22 files changed, 22 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb index a9cf345767..447fdcc2f1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-2.0.17-goolf-1.4.10.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 57fad2e4e7..3cc61b8643 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index 04a48d1f60..f64ca17dc1 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index 34c32694d7..ad92c7352d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index eda95916d0..c2159638f2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -19,7 +19,6 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index ab4f378feb..0db2cb2232 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index 92042e0a82..ad65bdfc92 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb index 5e8553cde7..8868b07c82 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb index bf81409418..0a2271f035 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb index 934d581d37..0dd48816d2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb index 890a8a4839..9e7b9cf60d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 024205f8b6..7cbefdf8ab 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb index bca769f27d..81edc7d68b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb index ab03a385a5..b3c186165b 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index 9cca953ebc..d9a3a23dd0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb index d9ce74d1cf..fcb13a817f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-intel-2015a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb index 5ec6f45b74..8648dbd440 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb index ec09959b74..59832233f0 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb @@ -18,7 +18,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb index 6d4de9bbd8..d79ef2b7af 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb index a45d43c1fa..7d8ebf1a32 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-foss-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb index 16eecd14b8..499d24c76f 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2015b.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb index 5e2d4fc5a2..f02fff458c 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.7-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 01924fc6212f07e9a18cd600576f2a1672ee8442 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 16:46:57 +0200 Subject: [PATCH 0775/2403] quickfix --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb index 76b32edded..10dacf3472 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-foss-2016a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] -patches = ['LASTZ-1.02.00_Makefile.patch'] +patches = ['LASTZ-%(version)s_Makefile.patch'] skipsteps = ['configure'] -- GitLab From aacbf6070779e6cd532ce03bea9aee2da65ddc87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:47:51 +0200 Subject: [PATCH 0776/2403] modify easyconfig PCL-1.7.2-intel-2016a-Python-2.7.11.eb, modify easyconfig VTK-6.3.0-intel-2016a-Python-2.7.11.eb --- .../easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb index 6c685288a4..2aa0797158 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -23,7 +23,7 @@ dependencies = [ ('Qhull', '2015.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts = '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index 1302e71e57..55d38284a0 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -33,7 +33,6 @@ sources = [ builddependencies = [('CMake', '3.5.2')] -mesaver = '11.0.8' dependencies = [ ('Python', '2.7.11'), ('libGLU', '9.0.0', '-Mesa-11.2.1'), -- GitLab From b83826fbddbf3a82d2852de3a0ff3b372d7cafb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 16:56:18 +0200 Subject: [PATCH 0777/2403] modify easyconfig Eigen-3.2.8-intel-2016a.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb index ec8373b9eb..3ba31dc38d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-intel-2016a.eb @@ -6,7 +6,6 @@ description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -- GitLab From 2cb4f18e397665dca42a2855989d8dc1c873f82d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:00:48 +0200 Subject: [PATCH 0778/2403] fix moduleclass in FLANN easyconfig --- .../f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb index 2072207364..82bf05536d 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -31,4 +31,4 @@ sanity_check_paths = { } sanity_check_commands = [('python', '-c "import pyflann"')] -moduleclass = '' +moduleclass = 'lib' -- GitLab From 85d18715306f40b7df042be06ace371577d0ddcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:03:13 +0200 Subject: [PATCH 0779/2403] check moduleclass for all easyconfigs --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index db5060f0b6..2d23e93e64 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -49,6 +49,7 @@ from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config +from easybuild.tools.config import build_option from easybuild.tools.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS @@ -263,8 +264,9 @@ def template_easyconfig_test(self, spec): fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) self.assertEqual(expected_subdir, subdir, fail_msg) - # sanity check for software name - self.assertTrue(ec['name'], name) + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) -- GitLab From 8d70f76effbf87f18b59050f70ab2ac317a87e10 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 9 May 2016 17:05:41 +0200 Subject: [PATCH 0780/2403] Set additional environment variables needed by MDSplus --- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 5 +++++ ...MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index b1dbee0965..111f00bfda 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index a5aa488ebe..25d836f8e5 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -27,4 +27,9 @@ preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' parallel = 1 +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + moduleclass = 'data' -- GitLab From e0ec35666ff58976a80b06e8f48abbdaecbee7fc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 17:25:00 +0200 Subject: [PATCH 0781/2403] GMAP-GSNAP with foss2016a --- .../GMAP-GSNAP-2016-05-01-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb new file mode 100644 index 0000000000..a44b2320e8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2016-04-04' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +#configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c0da370258d724be5c96dbdebecaf64eee8d6359 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 17:33:50 +0200 Subject: [PATCH 0782/2403] drop double line --- .../b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index 2abd2af08c..a42f248efe 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -12,7 +12,6 @@ name = 'Biopython' version = '1.65' versionsuffix = "-Python-%(pyver)s" - homepage = 'http://www.biopython.org' description = """Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to @@ -35,4 +34,4 @@ sanity_check_paths = { options = {'modulename': 'Bio'} -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From 48e0528837d5a104c655550c908631e367632b41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:00 +0200 Subject: [PATCH 0783/2403] add easyconfig FFmpeg-3.0.2-intel-2016a.eb --- .../f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb new file mode 100644 index 0000000000..fb0c75a29b --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From 6a9be36285ea30558bf51ebf212608de44f13806 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 May 2016 17:51:29 +0200 Subject: [PATCH 0784/2403] add easyconfig SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb --- ...iteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..63fe3bdb3b --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.2' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 083f6097e67a16f6817ca9d6f3cbfa7438b2ccc2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 9 May 2016 18:20:47 +0100 Subject: [PATCH 0785/2403] Add checksum and enforce renaming of tarball to EasyBuild standards --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index af32067597..eacaffe6ed 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -17,7 +17,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} # Registration required for download # http://www.openbioinformatics.org/annovar/annovar_download_form.php -sources = ['%(name)s.latest.tar.gz'] +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['2b26e514c54a847bfdcf4ce57e43f95c'] dependencies = [('Perl', '5.22.1')] -- GitLab From 013bc31badbb395d57449e5284215e61f826610d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 9 May 2016 19:10:28 +0100 Subject: [PATCH 0786/2403] add easyconfig FastQC-0.11.5-Java-1.7.0_80.eb, add easyconfig FastQC-0.11.5-Java-1.8.0_74.eb --- .../f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb | 32 +++++++++++++++++++ .../f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb new file mode 100644 index 0000000000..f6dbacc9e2 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb new file mode 100644 index 0000000000..7b8be6500d --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.8.0_74')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From fadd32eacf74fa74fd4e065d57704eedd9414853 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 10:55:45 +0200 Subject: [PATCH 0787/2403] version update --- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index a44b2320e8..84e054bf9c 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' -version = '2016-04-04' +version = '2016-05-01' homepage = 'http://research-pub.gene.com/gmap/' description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences -- GitLab From f449aad70457a4ebd314b927e634397c0f1822c4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 11:08:03 +0200 Subject: [PATCH 0788/2403] added newline --- easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index a4838ae3d0..9f8127a929 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -24,6 +24,7 @@ binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'c 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', 'update_status',] + sanity_check_paths = { 'files': ['bin/%s' % bin for binfile in binaries], 'dirs': ['bin'] -- GitLab From 2a0d756f82d1828bd5273bebcfa7afcd70405efa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:13:50 +0200 Subject: [PATCH 0789/2403] Add ESMF-7.0.0-foss-2016a.eb --- .../e/ESMF/ESMF-7.0.0-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb new file mode 100644 index 0000000000..c589117471 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-7.0.0-foss-2016a.eb @@ -0,0 +1,29 @@ +name = 'ESMF' +version = '7.0.0' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = ['ESMF-6.1.1_libopts.patch'] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.3'), + ('netCDF-C++', '4.2'), +] + +prebuildopts = 'ESMF_NETCDF_LIBS="`ncconfig --libs` `nf-config --flibs` `ncxx4-config --libs`" ' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ESMF_NETCDF_LIBS="`ncconfig --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' -- GitLab From cf69c6050935d504b0c9c4f02adc049658264197 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:25:25 +0200 Subject: [PATCH 0790/2403] Add netCDF/netCDF-4.4.0-foss-2016a.eb --- .../n/netCDF/netCDF-4.4.0-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb new file mode 100644 index 0000000000..39406d6275 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.47.0'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Doxygen', '1.8.11'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 786cde88a922411b67d07e0f550506e3fee7c0de Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:24:57 +0200 Subject: [PATCH 0791/2403] Add netCDF-Fortran-4.4.3-foss-2016a.eb --- .../netCDF-Fortran-4.4.3-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb new file mode 100644 index 0000000000..98a102fb28 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.3-foss-2016a.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.3' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From c115f4819900be51344d675f979f591b6614126d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 May 2016 11:24:35 +0200 Subject: [PATCH 0792/2403] Add netCDF-C++-4.2-foss-2016a.eb --- .../n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb new file mode 100644 index 0000000000..5f23071cc5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['netcdf-cxx-%(version)s.tar.gz'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +sanity_check_paths = { + 'files': ['include/ncvalues.h', 'include/netcdfcpp.h', 'include/netcdf.hh', 'lib/libnetcdf_c++.a', 'lib/libnetcdf_c++.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 40530fc95d74286b986af08eb4f7d9c7daeee848 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 12:24:21 +0200 Subject: [PATCH 0793/2403] added patch --- easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch new file mode 100644 index 0000000000..d5a95a417e --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch @@ -0,0 +1,11 @@ +--- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 ++++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 +@@ -246,7 +246,7 @@ + @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb + @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) + @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG +-AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ ++AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ + -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ + -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ + -std=c99 -- GitLab From b7381a539153e3f39aa2ef23704649522cc2a2bc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 10 May 2016 12:28:41 +0200 Subject: [PATCH 0794/2403] provided patch --- .../d/DIAL/DIAL-2011.06.06_Makefile.in.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch new file mode 100644 index 0000000000..0f365be126 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06_Makefile.in.patch @@ -0,0 +1,13 @@ +# Remove use of -Werror because Werror is not used (discussed in http://seqanswers.com/forums/showthread.php?t=20113). +# Using -Werror gives warnings which result in a failure of the installation. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG)--- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 ++++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 +@@ -246,7 +246,7 @@ + @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb + @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) + @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG +-AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ ++AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ + -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ + -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ + -std=c99 -- GitLab From fa6d81bf60bb2cb4f1f582a8577b718d0e151665 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:53:28 +0200 Subject: [PATCH 0795/2403] Change to bundle, include CGI --- .../BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 29 ++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index fdb264f023..3e3a66a690 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.6.924' @@ -10,21 +10,30 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] -sources = ['release-%s.tar.gz' % version.replace('.', '-')] +# this is a bundle of Perl modules packages +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") dependencies = [ ('Perl', '5.22.1'), ('DB_File', '1.835', versionsuffix), ] -#exts_list = [ -# ('CGI', '4.28', { -# 'source_tmpl': 'CGI-4.28.tar.gz', -# 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -# }), -#] +exts_list = [ + ('CGI', '4.28', { + 'source_tmpl': 'CGI-4.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + (name, version, { + 'modulename': 'Bio::Perl', + 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), + 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], + }), +] -options = {'modulename': 'Bio::Perl'} +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} moduleclass = 'bio' + -- GitLab From ea4d86d83894b1ec5cae01517b40c0a46df6f55d Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 12:56:36 +0200 Subject: [PATCH 0796/2403] Small change in comment --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 3e3a66a690..bd7bcac177 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -10,7 +10,7 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'foss', 'version': '2016a'} -# this is a bundle of Perl modules packages +# this is a bundle of Perl modules exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") -- GitLab From 5442266f3d9b5f6f62514c323f29b2dfd3724f96 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:02:34 +0200 Subject: [PATCH 0797/2403] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index bd7bcac177..796b828449 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,6 +20,7 @@ dependencies = [ ] exts_list = [ + # CGI has been removed from the Perl core since version 5.22. ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 6d2ee53436d7ffd21309097fd057bb8a99ddec77 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 10 May 2016 13:04:17 +0200 Subject: [PATCH 0798/2403] Comment about CGI --- .../b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 796b828449..d62e2cbb88 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ] exts_list = [ - # CGI has been removed from the Perl core since version 5.22. + # CGI has been removed from the Perl core since version 5.22 ('CGI', '4.28', { 'source_tmpl': 'CGI-4.28.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], -- GitLab From 08cf383bee8935e7091cdec693c1fbba153ae5cd Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 11:15:28 -0400 Subject: [PATCH 0799/2403] PGI: uncomment sanity checks; they now work with framework PR #1754 --- .../OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index be813ed50e..95cc4d76a5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -31,10 +31,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -#sanity_check_commands = [ -# ('mpicc --version | grep pgcc', ''), -# ('mpicxx --version | grep pgc++', ''), -# ('mpifort --version | grep pgfortran', ''), -#] +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] moduleclass = 'mpi' -- GitLab From a4703d9def18a0867167a45f1244c593099b1a79 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 10 May 2016 13:05:38 -0400 Subject: [PATCH 0800/2403] GraphicsMagick: add include/GraphicsMagick to CPATH as that is the include path. --- .../g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb | 2 ++ .../g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb index 513feabb7e..b7e2be06e2 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -14,4 +14,6 @@ source_urls = [ ] sources = [SOURCE_TAR_GZ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb index 6fa3747197..bd06dcc281 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-foss-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb index ea37c3e81c..de4cfae31e 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.23-intel-2016a.eb @@ -32,4 +32,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + moduleclass = 'vis' -- GitLab From 7184d0c0ddec1f80515700b43193c9721315b429 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:33:50 -0400 Subject: [PATCH 0801/2403] add easyconfig CGAL 4.8 for foss 2016a and dependencies --- .../CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb | 33 ++++++++++++++++ .../e/expat/expat-2.1.1-foss-2016a.eb | 16 ++++++++ .../fontconfig-2.11.95-foss-2016a.eb | 22 +++++++++++ .../intltool-0.51.0-foss-2016a-Perl-5.22.1.eb | 25 ++++++++++++ .../libxkbcommon-0.6.1-foss-2016a.eb | 32 +++++++++++++++ .../m/MPFR/MPFR-3.1.4-foss-2016a.eb | 26 +++++++++++++ .../easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb | 39 +++++++++++++++++++ .../XKeyboardConfig-2.17-foss-2016a.eb | 36 +++++++++++++++++ .../XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb | 27 +++++++++++++ .../xcb-util-image-0.4.0-foss-2016a.eb | 23 +++++++++++ .../xcb-util-keysyms-0.4.0-foss-2016a.eb | 24 ++++++++++++ .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 23 +++++++++++ .../xcb-util-wm-0.4.1-foss-2016a.eb | 23 +++++++++++ .../x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 24 ++++++++++++ 14 files changed, 373 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f4633df398 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e31e7039b5cdc74ac7b106db8ba644f3'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.4'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..1a58effe3d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.1-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.1' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb new file mode 100644 index 0000000000..93a5699fb5 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.95-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.11.95' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.1'), + ('freetype', '2.6.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..e0b8aa4117 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.22.1' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb new file mode 100644 index 0000000000..5f450a0988 --- /dev/null +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxkbcommon' +version = '0.6.1' + +homepage = 'http://xkbcommon.org/' +description = """xkbcommon is a library to handle keyboard descriptions, + including loading them from disk, parsing them and handling their state. + It's mainly meant for client toolkits, window systems, + and other system applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xkbcommon.org/download/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libxcb', '1.11.1'), + ('XKeyboardConfig', '2.17'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': ['lib/libxkbcommon%s.so' % x for x in ['', '-x11']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb new file mode 100644 index 0000000000..fe347368b1 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.0')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb new file mode 100644 index 0000000000..27b1514a37 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.6.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb new file mode 100644 index 0000000000..10d7fbd3ea --- /dev/null +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'XKeyboardConfig' +version = '2.17' + +homepage = 'http://www.freedesktop.org/wiki/Software/XKeyboardConfig/' +description = """The non-arch keyboard configuration database for X Window. + The goal is to provide the consistent, well-structured, + frequently released open source of X keyboard configuration data + for X Window System implementations (free, open source and commercial). + The project is targeted to XKB-based systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.x.org/pub/individual/data/xkeyboard-config/'] +sources = ['xkeyboard-config-%(version)s.tar.bz2'] + +builddependencies = [ + ('libxslt', '1.1.28'), + ('gettext', '0.19.7'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +# see http://www.linuxfromscratch.org/blfs/view/svn/x/xkeyboard-config.html +configopts = '--with-xkb-rules-symlink=xorg ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/X11/xkb'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..71416dbf17 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1'), + ('expat', '2.1.1') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..bb023fe417 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-image' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-image package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('xcb-util', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-image.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..000b28f309 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-keysyms' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-keysyms package contains a library for + handling standard X key constants and conversion to/from keycodes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-keysyms.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb new file mode 100644 index 0000000000..fd3484fb38 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-renderutil' +version = '0.3.9' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-renderutil package provides additional extensions to the XCB library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-render-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb new file mode 100644 index 0000000000..d412a4babf --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util-wm' +version = '0.4.1' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-%s.so' % x for x in ['ewmh', 'icccm']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb new file mode 100644 index 0000000000..78a0c3a9b7 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-util' +version = '0.4.0' + +homepage = 'http://xcb.freedesktop.org/' +description = """The xcb-util package provides additional extensions to the XCB library, + many that were previously found in Xlib, but are not part of core X protocol""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxcb', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb-util.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From dfabd2e04531e4f26aa54f3d487e36da8774b93c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Tue, 10 May 2016 15:40:40 -0400 Subject: [PATCH 0802/2403] add easyconfig boost_versionsuffix --- .../Boost-1.60.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a913c20849 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 37dfc06cc929c2bd313f65dcd50f57a08f6dedc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 09:36:09 +0200 Subject: [PATCH 0803/2403] clean up dummy bzip2 easyconfig, define buildopts rather than defining and via os.environ --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 4d95eeaef2..7ae9aaf98a 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -12,8 +12,8 @@ toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bzip.org/%(version)s/'] -import os -os.environ['CC'] = 'gcc' -os.environ['CFLAGS'] = '-O3 -fPIC' +buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" + +with_shared_libs = False moduleclass = 'tools' -- GitLab From f6d376f8e12af48220b36c23b3542df2d1a15bd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 09:37:39 +0200 Subject: [PATCH 0804/2403] clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 7ae9aaf98a..460cd7abe7 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -14,6 +14,7 @@ source_urls = ['http://www.bzip.org/%(version)s/'] buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" +# disable building of shared libraries, doesn't work everywhere (e.g. on OS X, where 'gcc' is actually Clang...) with_shared_libs = False moduleclass = 'tools' -- GitLab From cd98ac1f5b3372ad1346ce99048059b4ed435a40 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 11 May 2016 12:34:44 +0200 Subject: [PATCH 0805/2403] Include patch that fixes bug in build-score/configure, which breaks builds involving multiple toolchains (e.g., compiling Score-P for Intel against Cube built with GGGcore) --- .../s/Score-P/Score-P-2.0.1-foss-2016a.eb | 7 +++ .../Score-P-2.0.1_fix_score_configure.patch | 52 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 66303634bd..feeade9e0a 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -24,8 +24,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['scorep-%(version)s.tar.gz'] source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +# Backported fix to prevent build-score/configure from picking up CFLAGS etc.; +# included in Score-P 2.0.2 and above +patches = [ + 'Score-P-2.0.1_fix_score_configure.patch', +] + checksums = [ '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz + 'e5bfc115b9013b87a294a3bd84db02ed', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch new file mode 100644 index 0000000000..c387be0132 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch @@ -0,0 +1,52 @@ +--- build-score/configure.orig 2016-05-11 09:21:03.716441529 +0200 ++++ build-score/configure 2016-05-11 09:38:14.651525955 +0200 +@@ -735,6 +735,7 @@ afs_srcdir + AFS_PACKAGE_TO_TOP + AFS_PACKAGE_NAME + AFS_PACKAGE_name ++CXXFLAGS_FOR_BUILD_SCORE + target_alias + host_alias + build_alias +@@ -790,6 +791,7 @@ enable_libtool_lock + ac_precious_vars='build_alias + host_alias + target_alias ++CXXFLAGS_FOR_BUILD_SCORE + CC + CFLAGS + LDFLAGS +@@ -1444,6 +1446,8 @@ Optional Packages: + compiler's sysroot if not specified). + + Some influential environment variables: ++ CXXFLAGS_FOR_BUILD_SCORE ++ C++ compiler flags for building scorep-score + CC C compiler command + CFLAGS C compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a +@@ -2363,6 +2367,24 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu + + + ++# Compilers etc. are set according to Cube installation (see below), ++# so ignore environment variables set in the environment. ++{ CC=; unset CC;} ++{ CFLAGS=; unset CFLAGS;} ++{ LDFLAGS=; unset LDFLAGS;} ++{ LIBS=; unset LIBS;} ++{ CPPFLAGS=; unset CPPFLAGS;} ++{ LT_SYS_LIBRARY_PATH=; unset LT_SYS_LIBRARY_PATH;} ++{ CPP=; unset CPP;} ++{ CXX=; unset CXX;} ++{ CXXFLAGS=; unset CXXFLAGS;} ++{ CXXCPP=; unset CXXCPP;} ++ ++ ++if test "x${ac_cv_env_CXXFLAGS_FOR_BUILD_SCORE_set}" = xset; then : ++ CXXFLAGS="${ac_cv_env_CXXFLAGS_FOR_BUILD_SCORE_value}" ++fi ++ + + + -- GitLab From a7042f4afe607a698be30c08bcd74918118486df Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 11 May 2016 12:48:07 +0200 Subject: [PATCH 0806/2403] Bump PDT to 3.22 --- .../p/PDT/{PDT-3.21-foss-2016a.eb => PDT-3.22-foss-2016a.eb} | 4 ++-- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PDT/{PDT-3.21-foss-2016a.eb => PDT-3.22-foss-2016a.eb} (92%) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb similarity index 92% rename from easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb rename to easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb index a48bf0f63e..c1c3137a73 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb @@ -11,7 +11,7 @@ ## name = 'PDT' -version = '3.21' +version = '3.22' homepage = 'http://www.cs.uoregon.edu/research/pdt/' description = """Program Database Toolkit (PDT) is a framework for analyzing source @@ -26,7 +26,7 @@ sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] checksums = [ - '3092ca0d8833b69992c17e63ae66c263', # pdtoolkit-3.21.tar.gz + '982d667617802962a1f7fe6c4c31184f', # pdtoolkit-3.22.tar.gz ] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index feeade9e0a..c013f5f3e6 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -43,7 +43,7 @@ dependencies = [ ('OPARI2', '2.0'), ('OTF2', '2.0'), ('PAPI', '5.4.3'), - ('PDT', '3.21'), + ('PDT', '3.22'), ] configopts = '--enable-shared' -- GitLab From 6569ffa0d96ffcf7dfe5545df6567d0eb19d2b51 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 14:00:02 +0200 Subject: [PATCH 0807/2403] {bio}[foss-2016a] Kraken 0.10.5-beta (REVIEW) --- .../Jellyfish/Jellyfish-1.1.11-foss-2016a.eb | 25 +++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 43 +++++++++++++++++++ .../Kraken/Kraken_0.10.5-beta_makefile.patch | 12 ++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb new file mode 100644 index 0000000000..8e2a518511 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.11' + +homepage = 'http://www.cbcb.umd.edu/software/jellyfish/' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.cbcb.umd.edu/software/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..ad490e94ef --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '0.10.5-beta' +versionsuffix='-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/kraken/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +#Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://ccb.jhu.edu/software/kraken/dl/'] +sources = [SOURCELOWER_TGZ] + +patches = ['Kraken_%(version)s_makefile.patch'] + +dependencies = [ + ('Perl', '5.22.1'), + ('Jellyfish', '1.1.11'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch new file mode 100644 index 0000000000..4a0bc26aa6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken_0.10.5-beta_makefile.patch @@ -0,0 +1,12 @@ +#Pick CXX and CXXFLAGS from EasyBuild via pre-defined variables +#May 11th 2016 by B. Hajgato (Free Uninrrsity Brussels, VUB) +--- kraken-0.10.5-beta/src/Makefile.orig 2015-02-18 12:38:00.000000000 +0100 ++++ kraken-0.10.5-beta/src/Makefile 2016-05-11 13:33:39.370016057 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -Wall -fopenmp -O3 ++CXX ?= g++ ++CXXFLAGS ?= -Wall -fopenmp -O3 + PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink + + .PHONY: all install clean -- GitLab From e6a548baeec911151b309f32cc10404060136fb6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 15:04:52 +0200 Subject: [PATCH 0808/2403] Add OpenSSL-1.0.2g-GCCcore-4.9.3.eb to work with minimal toolchains --- .../o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..29256de39d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.2g' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From ee694e1b8f698196b590aaee777130a1feb3de1f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:09:49 +0200 Subject: [PATCH 0809/2403] Add tmux-2.2-GCCcore-4.9.3.eb --- .../t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..a8b6500ba3 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.2' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 8a22b902332cf5110c9055b9df18c2d720522d93 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 11 May 2016 16:10:06 +0200 Subject: [PATCH 0810/2403] Add libevent-2.0.22-GCCcore-4.9.3.eb --- .../libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..2de9d3663c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.25', '', True), +] + +moduleclass = 'lib' -- GitLab From f280305bef61512ee04bf405afee98cb1d9e2802 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:20:40 +0200 Subject: [PATCH 0811/2403] add wget dependency to Kraken --- .../g/gnutls/gnutls-3.4.11-foss-2016a.eb | 40 +++++++++++++++++++ .../g/guile/guile-1.8.8-foss-2016a.eb | 32 +++++++++++++++ ...aken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 1 + .../l/libidn/libidn-1.32-foss-2016a.eb | 19 +++++++++ .../l/libtasn1/libtasn1-4.7-foss-2016a.eb | 22 ++++++++++ .../libunistring-0.9.3-foss-2016a.eb | 24 +++++++++++ .../n/nettle/nettle-3.1.1-foss-2016a.eb | 28 +++++++++++++ .../p/p11-kit/p11-kit-0.23.2-foss-2016a.eb | 29 ++++++++++++++ .../w/wget/wget-1.17.1-foss-2016a.eb | 35 ++++++++++++++++ 9 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb new file mode 100644 index 0000000000..fbf5215dd8 --- /dev/null +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gnutls' +version = '3.4.11' + +homepage = 'http://www.gnutls.org/' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCE_TAR_XZ] + +guilever = '1.8.8' +guileshortver = '.'.join(guilever.split('.')[:2]) +dependencies = [ + ('GMP', '6.1.0'), + ('nettle', '3.1.1'), + ('guile', guilever), + ('libtasn1', '4.7'), + ('libidn', '1.32'), + ('p11-kit', '0.23.2'), +] + +configopts = "--with-guile-site-dir=$EBROOTGUILE --enable-openssl-compatibility " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'crywrap', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]] + + ['lib/guile/%s/guile-gnutls-v-2.so' % guileshortver], + 'dirs': ['include/gnutls'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb new file mode 100644 index 0000000000..132fe56abf --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.0'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.29'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index ad490e94ef..4bb09cbfe2 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -25,6 +25,7 @@ patches = ['Kraken_%(version)s_makefile.patch'] dependencies = [ ('Perl', '5.22.1'), ('Jellyfish', '1.1.11'), + ('wget', '1.17.1'), ] install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb new file mode 100644 index 0000000000..be095e8cc2 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb new file mode 100644 index 0000000000..0a37b2e392 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.7-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.7' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. + It was written by Fabio Fiorina, and has been shipped as part of GnuTLS + for some time but is now a proper GNU package.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb new file mode 100644 index 0000000000..052063704a --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb new file mode 100644 index 0000000000..fc3be53324 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.1.1' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb new file mode 100644 index 0000000000..75ecf0ad6a --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.23.2' + +homepage = 'http://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://p11-glue.freedesktop.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libtasn1', '4.7'), + ('libffi', '3.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb new file mode 100644 index 0000000000..855ecb2068 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.17.1' + +homepage = 'https://www.gnu.org/software/wget/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('gnutls', '3.4.11'), + ('PCRE', '8.38'), + ('libidn', '1.32'), + ('zlib', '1.2.8'), + #('OpenSSL', '1.0.1s'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +#Optionally, you can use OpenSSL insted of gnutls +#configopts = '--with-ssl=openssl ' +# +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/wget'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 7a5bbbf4be73ddcce4a1e18aa9dd2363fb5ce7f7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2016 16:32:43 +0200 Subject: [PATCH 0812/2403] use os dep gnutls --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 855ecb2068..6ca8a613aa 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -14,7 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] dependencies = [ - ('gnutls', '3.4.11'), + #('gnutls', '3.4.11'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date gnutls for security reasons ('PCRE', '8.38'), ('libidn', '1.32'), ('zlib', '1.2.8'), @@ -26,6 +27,7 @@ dependencies = [ #configopts = '--with-ssl=openssl ' # #osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('gnutls')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From 38cacab3b3d32d4b13267a167a6681e01a122d8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:18 +0200 Subject: [PATCH 0813/2403] add easyconfig Wannier90-2.0.1-intel-2016a.eb --- .../Wannier90/Wannier90-2.0.1-intel-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb new file mode 100644 index 0000000000..5f4964f921 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.0.1-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.0.1' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] + +patches = ['Wannier90_2x_ignore_makesys.patch'] + +prebuildopts = 'F90=$F90 COMMS=mpi MPIF90=mpiifort FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +prebuildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' + +# build program and library +buildopts = "all" + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 47ee49d3fe6431cb7a0f1b20a8778569f9c5db65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 16:53:43 +0200 Subject: [PATCH 0814/2403] add easyconfig FLEUR-0.26e-intel-2016a.eb --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb new file mode 100644 index 0000000000..39ac2cdb63 --- /dev/null +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'FLEUR' +version = '0.26e' + +homepage = 'http://www.flapw.de/' +description = """FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, + based on density-functional theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +# dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads +sources = ['v%s.tgz' % version.split('.')[1]] + +builddependencies = [('imake', '1.0.7')] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), + ('HDF5', '1.8.16'), +# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile +] + +# define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') +prebuildopts = "sed -i 's/^#define jureca/#define linux_evp_64/g' Imakefile && " +# don't specialize for systems with structural symmetry +prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " +# no need to jump through hoops to make compilation work with older Fortran compilers +prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " + +prebuildopts += "imake && " +buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' + +# parallel build tends to fail +parallel = 1 + +files_to_copy = [(['fleur.x', 'inpgen.x'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fleur.x', 'bin/inpgen.x'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From d4b275db57e76944ce1f2ffd4e54e9610ef7f221 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 12:19:16 -0400 Subject: [PATCH 0815/2403] improve Yade easyconfig --- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 45 ++++++------------- 1 file changed, 13 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 5e5fa25372..6f3e1611f8 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -18,53 +18,34 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), - ('GL2PS', '1.3.9'), - ('Python', '2.7.11'), + ('GL2PS', '1.3.9', '-Mesa-11.2.1'), + ('Python', '2.7.11'), ('IPython', '3.2.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), ('Eigen', '3.2.7'), ('minieigen', '0.5.3', versionsuffix), - ('Qt', '4.8.7'), + ('Qt', '4.8.7', '-GLib-2.48.0'), ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3'), - ('GDB', '7.10.1', versionsuffix), - ('zlib', '1.2.8'), - # optional -# ('CGAL', '4.7'), + ('libQGLViewer', '2.6.3', '-Mesa-11.2.1'), + ('zlib', '1.2.8'), + ('CGAL', '4.8', versionsuffix), ] -builddependencies = [('CMake', '3.4.3')] +builddependencies = [('CMake', '3.5.2')] separate_build_dir = True configopts = '-DENABLE_GUI=OFF ' configopts += '-DENABLE_VTK=OFF ' -configopts += '-DENABLE_CGAL=OFF' configopts += '-DENABLE_LINSOLV=OFF ' configopts += '-DENABLE_PFVFLOW=OFF ' -configopts += '-DQGLVIEWER_INCLUDE_DIR=$EBROOTLIBQGLVIEWER/include ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include ' +configopts += '-DGMP_LIBRARIES=$EBROOTGMP/lib ' +configopts += '-DGMPXX_LIBRARIES=$EBROOTGMP/lib ' -# In case you want disable some Yade features -# configopts = '-OPTION_1 = OFF -OPTION_2 = OFF ...' - -# options available, -# ENABLE_GUI: enable GUI option (ON by default) -# ENABLE_CGAL: enable CGAL option (ON by default) -# ENABLE_VTK: enable VTK-export option (ON by default) -# ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) -# ENABLE_GTS: enable GTS-option (ON by default) -# ENABLE_GL2PS: enable GL2PS-option (ON by default) -# ENABLE_LINSOLV: enable LINSOLV-option (ON by default) -# ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) -# ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) -# ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) -# ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) -# ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) -# ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) -# runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) -# CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) -# VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) -# USE_QT5: use QT5 for GUI, experimental (OFF by default) +#to disable CGAL uncomment the following line: +#configopts += '-DENABLE_CGAL=OFF ' sanity_check_paths = { 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], -- GitLab From b34283cba9fb1d3ccea409d2e7fc8a885fe13d30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 20:30:33 +0200 Subject: [PATCH 0816/2403] fix remark, enable r8 toolchain option, add imake easyconfig to resolve dep --- .../f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 4 ++-- .../i/imake/imake-1.0.7-intel-2016a.eb | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index 39ac2cdb63..d7d711211d 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -8,7 +8,7 @@ description = """FLEUR is a feature-full, freely available FLAPW (full potential based on density-functional theory.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'r8': True} # dowload requires registration, see http://www.flapw.de/pm/index.php?n=FLEUR.Downloads sources = ['v%s.tgz' % version.split('.')[1]] @@ -30,7 +30,7 @@ prebuildopts += "sed -i 's/^#define inversion//g' Imakefile && " prebuildopts += "sed -i 's/^#define f_90//g' Imakefile && " prebuildopts += "imake && " -buildopts = 'FC="$FC" FFLAGS="$FFLAGS -r8 -assume byterecl" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' +buildopts = 'FC="$FC" FFLAGS="$FFLAGS" HDFROOT=$EBROOTHDF5 fleur.x inpgen.x' # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb new file mode 100644 index 0000000000..dd473f56b9 --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.7-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.7' + +homepage = 'http://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it easier to develop software + portably for multiple systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://artfiles.org/x.org/pub/individual/util/'] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', + 'mkdirhier', 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 0129924d39247c5ade82b7d9a4a32b9f41557ec8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 21:59:27 +0200 Subject: [PATCH 0817/2403] {toolchain}[pompi/2016.04] HPL 2.1 --- .../h/HPL/HPL-2.1-pomkl-2016.04.eb | 23 +++++++++++ .../hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb | 22 ++++++++++ .../i/imkl/imkl-11.3.3.210-pompi-2016.04.eb | 36 +++++++++++++++++ .../n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb | 25 ++++++++++++ .../OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 40 +++++++++++++++++++ .../p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb | 25 ++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.04.eb | 20 ++++++++++ .../easyconfigs/p/pompi/pompi-2016.04.eb | 19 +++++++++ 8 files changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.04.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb new file mode 100644 index 0000000000..7d18ed0de8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -0,0 +1,23 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'pomkl', 'version': '2016.04'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +# needs to include -ldl or else we get +# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' +import os +os.environ['LIBS'] = '-ldl' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..1b876ae44f --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +# numactl is a direct dependency of PGI +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb new file mode 100644 index 0000000000..ab281bf6b1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'pompi', 'version': '2016.04'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb new file mode 100644 index 0000000000..a7cf283740 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.26')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..017a48c7e4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.3')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb new file mode 100644 index 0000000000..09bd42b128 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.4' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['3804dc13b8cf3d50aa16fb56e2682dd7'] + +gccver = '5.3.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb new file mode 100644 index 0000000000..1c27eb7962 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.04' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.4' +gccsuff = '-GCC-5.3.0-2.26' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb new file mode 100644 index 0000000000..b7e500bb5f --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.04' +pgisuffix = '-GCC-5.3.0-2.26' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.4' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.2', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From 8bad3a4379147aea0fe99cdf2b994dc67c053ce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2016 22:01:45 +0200 Subject: [PATCH 0818/2403] drop duplicate empty line --- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 1 - .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 95cc4d76a5..3dfb0c023b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 017a48c7e4..274fb15e1f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -- GitLab From 99a8ea6b43e676485d7a62cdc44c389bfd1d78ff Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 17:07:44 -0400 Subject: [PATCH 0819/2403] compiler finds eigen include-path automatic, no needs patch --- ...inieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 5 +--- .../m/minieigen/minieigen-0.5.3_Eigen.patch | 24 ------------------- 2 files changed, 1 insertion(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index bcc3a6db18..6bb8c242f7 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'minieigen' version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://launchpad.net/minieigen/' description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" @@ -11,10 +12,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] -patches = ['minieigen-0.5.3_Eigen.patch'] - -versionsuffix = '-Python-%(pyver)s' - dependencies = [ ('Boost', '1.60.0', versionsuffix), ('Eigen', '3.2.7'), diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch deleted file mode 100644 index 95775909f2..0000000000 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3_Eigen.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru minieigen-0.5.3.orig/setup.py minieigen-0.5.3/setup.py ---- minieigen-0.5.3.orig/setup.py 2015-09-18 12:15:40.000000000 -0400 -+++ minieigen-0.5.3/setup.py 2016-04-28 14:12:46.507198765 -0400 -@@ -1,6 +1,6 @@ - # encoding: utf-8 - from distutils.core import setup,Extension --import sys, glob -+import os, sys, glob - - # vectorization is currently broken and experimental ONLY - vectorize=False -@@ -19,10 +19,11 @@ - # * https://bugs.launchpad.net/panda3d/+bug/919237 - define_macros+=[('EIGEN_DONT_VECTORIZE',None)] - else: -+ eigen_prefix = os.environ.get('EBROOTEIGEN', 'EBROOTEIGEN_NOT_DEFINED') - py3k=(sys.version_info[0]==3) - libraries=['boost_python-py3%d'%sys.version_info[1] if py3k else 'boost_python'] - library_dirs=[] -- include_dirs=['/usr/include/eigen3','/usr/local/include/eigen3','minieigen'] -+ include_dirs=['%s/include/eigen3' % eigen_prefix, 'minieigen'] - - setup(name='minieigen', - version='0.5.3', -- GitLab From 9fdbee0e78675e3587889e8fd9f5a1ea20fdf256 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Wed, 11 May 2016 17:10:39 -0400 Subject: [PATCH 0820/2403] improve Yade and Loki easyconfig --- .../l/Loki/Loki-0.1.7-foss-2016a.eb | 7 ++++--- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 20 +++++++------------ 2 files changed, 11 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index 990683c5b7..07ee053893 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -4,17 +4,18 @@ name = 'Loki' version = '0.1.7' homepage = 'http://loki-lib.sourceforge.net/' -description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms. """ +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ toolchain = {'name': 'foss', 'version': '2016a'} -installopts = "prefix=%(installdir)s" - source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] sources = [SOURCELOWER_TAR_GZ] skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" + sanity_check_paths={ 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 6f3e1611f8..6ca7251d44 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -15,10 +15,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] sources = [SOURCELOWER_TAR_GZ] +mesaver = '11.2.1' dependencies = [ ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), - ('GL2PS', '1.3.9', '-Mesa-11.2.1'), + ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), ('Python', '2.7.11'), ('IPython', '3.2.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), @@ -26,7 +27,7 @@ dependencies = [ ('minieigen', '0.5.3', versionsuffix), ('Qt', '4.8.7', '-GLib-2.48.0'), ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3', '-Mesa-11.2.1'), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), ('zlib', '1.2.8'), ('CGAL', '4.8', versionsuffix), ] @@ -35,20 +36,13 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF ' -configopts += '-DENABLE_VTK=OFF ' -configopts += '-DENABLE_LINSOLV=OFF ' -configopts += '-DENABLE_PFVFLOW=OFF ' +configopts = '-DENABLE_GUI=OFF -DENABLE_VTK=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' -configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include ' -configopts += '-DGMP_LIBRARIES=$EBROOTGMP/lib ' -configopts += '-DGMPXX_LIBRARIES=$EBROOTGMP/lib ' - -#to disable CGAL uncomment the following line: -#configopts += '-DENABLE_CGAL=OFF ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], } -- GitLab From ffd9ea76ab826db4b79c77d1901733df17239d59 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 07:38:23 +0200 Subject: [PATCH 0821/2403] Use OpenSSL --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 6ca8a613aa..969681ed3b 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -23,11 +23,11 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -#Optionally, you can use OpenSSL insted of gnutls -#configopts = '--with-ssl=openssl ' -# -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -osdependencies = [('gnutls')] +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From f4491d2ac003c2e3b16e422b837043762403c720 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:29:40 +0200 Subject: [PATCH 0822/2403] Type corrected in the comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 969681ed3b..462167df50 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,8 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL -#osdependencies = [('gnutls-devel', 'gnutls-dev), 'libgnutls-devel')] +#Optionally, you can use gnutls (default) instead of OpenSSL +#osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], -- GitLab From b4850c38476a83f68723becde0c0d16646849551 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 May 2016 09:32:05 +0200 Subject: [PATCH 0823/2403] extra comment --- easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index 462167df50..bbebd9aa83 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -26,7 +26,8 @@ dependencies = [ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -#Optionally, you can use gnutls (default) instead of OpenSSL +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. #osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { -- GitLab From a8c17069e073d203c1187cef09c1495efe2c33d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 10:19:12 +0200 Subject: [PATCH 0824/2403] remove hack in HPL pomkl easyconfig for linking with -ldl --- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb index 73bc06cddb..9552b4d653 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -15,9 +15,4 @@ source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] -# needs to include -ldl or else we get -# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' -import os -os.environ['LIBS'] = '-ldl' - moduleclass = 'tools' -- GitLab From 3fbfc03ba64a14c5c803d6761009142a490e5015 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 10:57:41 +0200 Subject: [PATCH 0825/2403] {chem}[intel/2016a] NBO 1.1 --- .../easyconfigs/n/NBO/NBO-1.1_MKL95.patch | 505 ++++++++++++++++++ easybuild/easyconfigs/n/NBO/NBO.eb | 27 + 2 files changed, 532 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch create mode 100644 easybuild/easyconfigs/n/NBO/NBO.eb diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch new file mode 100644 index 0000000000..1bde9b006b --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1_MKL95.patch @@ -0,0 +1,505 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru periodic_nbo.orig/matutil.f90 periodic_nbo/matutil.f90 +--- periodic_nbo.orig/matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/matutil.f90 2016-05-12 10:17:54.673546000 +0200 +@@ -93,7 +93,7 @@ + END FUNCTION matdet + + FUNCTION matsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matsqrt_real, vecs +@@ -115,14 +115,14 @@ + FORALL (i=1:n1) matsqrt_real(i,i) = SQRT(abs(vals(i))) + !matsqrt_real = MATMUL(vecs, MATMUL(matsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matsqrt_real,'N','T',1.d0,0.d0) + + + END FUNCTION matsqrt_real + + FUNCTION matsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matsqrt_complex, vecs +@@ -140,13 +140,13 @@ + FORALL (i=1:n1) matsqrt_complex(i,i) = SQRT(abs(vals(i))) + !matsqrt_complex = MATMUL(vecs, MATMUL(matsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matsqrt_complex + + FUNCTION matinvsqrt_real(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinvsqrt_real, vecs +@@ -164,13 +164,13 @@ + FORALL (i=1:n1) matinvsqrt_real(i,i) = 1.d0/SQRT(abs(vals(i))) + !matinvsqrt_real = MATMUL(vecs, MATMUL(matinvsqrt_real, TRANSPOSE(vecs))) + +- CALL DGEMM_MKL95(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matinvsqrt_real,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matinvsqrt_real,'N','T',1.d0,0.d0) + + END FUNCTION matinvsqrt_real + + FUNCTION matinvsqrt_complex(cmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinvsqrt_complex, vecs +@@ -199,13 +199,13 @@ + + !matinvsqrt_complex = MATMUL(vecs, MATMUL(matinvsqrt_complex, TRANSPOSE(CONJG(vecs)))) + +- CALL ZGEMM_MKL95(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(vecs,matinvsqrt_complex,dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(dummy,vecs,matinvsqrt_complex,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + END FUNCTION matinvsqrt_complex + + FUNCTION matexp(dmat) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matexp, vecs +@@ -222,8 +222,8 @@ + matexp = 0.d0 + FORALL (i=1:n1) matexp(i,i) = EXP(vals(i)) + !matexp = MATMUL(vecs, MATMUL(matexp, TRANSPOSE(vecs))) +- CALL DGEMM_MKL95(vecs,matexp,dummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,vecs,matexp,'N','T',1.d0,0.d0) ++ CALL DGEMM(vecs,matexp,dummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(dummy,vecs,matexp,'N','T',1.d0,0.d0) + + END FUNCTION matexp + +@@ -246,8 +246,8 @@ + + ! solves the generalized eigenvalue equations D c=S c*lambda + SUBROUTINE diag_general(dmat,smat,dvals,dvecs) +- USE MKL95_BLAS +- USE MKL95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat, smat, dvecs + REAL*8 , DIMENSION(:) :: dvals +@@ -277,14 +277,14 @@ + + ! transform to the coordinates of the normal eigensystem + !dmat = MATMUL(TRANSPOSE(shalfi),MATMUL(dmat,shalfi)) +- CALL DGEMM_MKL95(shalfi,dmat,dummy,'T','N',1.d0,0.d0) +- CALL DGEMM_MKL95(dummy,shalfi,dmat,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dmat,dummy,'T','N',1.d0,0.d0) ++ CALL DGEMM(dummy,shalfi,dmat,'N','N',1.d0,0.d0) + ! get the normal eigenvalues and vectors + call jacobi(dmat,n1,n1,dvals,dvecs,nrot) + ! transform the eigenvectors BACK to the original coordinate system + !dvecs = MATMUL(shalfi, dvecs) + dummy = dvecs +- CALL DGEMM_MKL95(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) ++ CALL DGEMM(shalfi,dummy,dvecs,'N','N',1.d0,0.d0) + CALL eigsrt(dvals,dvecs,n1,n1) + + !WRITE(6,*)'Eigenvalues' +@@ -294,7 +294,7 @@ + END SUBROUTINE diag_general + + FUNCTION matinv_real(dmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1),SIZE(dmat,2)) :: matinv_real +@@ -306,12 +306,12 @@ + IF (n1.NE.n2) STOP 'Attempting to invert a non-square matrix' + + matinv_real=dmat +- CALL DGETRF_MKL95(matinv_real,ipiv,info) +- CALL DGETRI_MKL95(matinv_real,ipiv,info) ++ CALL DGETRF(matinv_real,ipiv,info) ++ CALL DGETRI(matinv_real,ipiv,info) + END FUNCTION matinv_real + + FUNCTION matinv_complex(cmat) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + COMPLEX*16 , DIMENSION(SIZE(cmat,1),SIZE(cmat,2)) :: matinv_complex +@@ -328,7 +328,7 @@ + + + !evecs = cmat +- !CALL ZHEEV_MKL95(evecs,evals,'V','U',INFO) ++ !CALL ZHEEV(evecs,evals,'V','U',INFO) + !DO info=1,SIZE(evals,1) + ! WRITE(6,'(F10.5)')evals(info) + !ENDDO +@@ -337,8 +337,8 @@ + + + matinv_complex=cmat +- CALL ZGETRF_MKL95(matinv_complex,ipiv,info) +- CALL ZGETRI_MKL95(matinv_complex,ipiv,info) ++ CALL ZGETRF(matinv_complex,ipiv,info) ++ CALL ZGETRI(matinv_complex,ipiv,info) + END FUNCTION matinv_complex + + FUNCTION outer_product(x,y) +@@ -351,7 +351,7 @@ + + !Fortran 90 wrappers for diag routines + SUBROUTINE matdiag_real(dmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + REAL*8 , DIMENSION(:,:) :: dmat + REAL*8 , DIMENSION(SIZE(dmat,1)) :: evals +@@ -363,7 +363,7 @@ + IF (n1.NE.n2) STOP 'Attempting to diagonalize a non-square matrix' + + evecs=dmat +- !CALL dsyev_mkl95(evecs,evals,'V','U',info) ++ !CALL dsyev(evecs,evals,'V','U',info) + CALL diag(dmat,n1,n1,evals,evecs) + + !WRITE(6,*)'using real symmetrizing routine' +@@ -373,7 +373,7 @@ + END SUBROUTINE matdiag_real + + SUBROUTINE matdiag_complex(cmat,evals,evecs) +- USE MKL95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + COMPLEX*16 , DIMENSION(:,:) :: cmat + REAL*8 , DIMENSION(SIZE(cmat,1)) :: evals +@@ -389,11 +389,11 @@ + + evecs=cmat + +- CALL zheev_mkl95(evecs,evals,'V','U',info) ++ CALL zheev(evecs,evals,'V','U',info) + IF (info.NE.0) STOP 'Error in matdiag_complex' + + !dummy=cmat +- !CALL ZGESVD_MKL95(dummy,sing_value,u_matrix,v_matrix) ++ !CALL ZGESVD(dummy,sing_value,u_matrix,v_matrix) + + + !IF( evals(1) .LE. -1.d-13 )WRITE(6,*)'WHOOOOOOOOOAAAAAAAAAAAAAAA!!! Negative eigenvalues' +@@ -436,31 +436,31 @@ + END FUNCTION matiden + + FUNCTION matunitary_trans_real(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: A,U + REAL*8,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + REAL*8,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL DGEMM_MKL95(A,U,dummy,'N','T',1.d0,0.d0) +- CALL DGEMM_MKL95(U,dummy,Ap,'N','N',1.d0,0.d0) ++ CALL DGEMM(A,U,dummy,'N','T',1.d0,0.d0) ++ CALL DGEMM(U,dummy,Ap,'N','N',1.d0,0.d0) + END FUNCTION matunitary_trans_real + + FUNCTION matunitary_trans_complex(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A,U + COMPLEX*16,DIMENSION(SIZE(U,1),SIZE(U,1)) :: Ap + COMPLEX*16,DIMENSION(SIZE(A,1),SIZE(U,1)) :: dummy + + !Ap=MATMUL(U,MATMUL(A,CONJG(TRANSPOSE(U)))) +- CALL ZGEMM_MKL95(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex + + FUNCTION matunitary_trans_complex2(A,U) RESULT(Ap) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + COMPLEX*16,DIMENSION(:,:) :: A + REAL*8,DIMENSION(:,:) :: U +@@ -470,8 +470,8 @@ + + U_comp = U + !Ap=MATMUL(U,MATMUL(A,TRANSPOSE(U))) +- CALL ZGEMM_MKL95(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(A,U_comp,dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(U_comp,dummy,Ap,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + END FUNCTION matunitary_trans_complex2 + + +diff -ru periodic_nbo.orig/nbo.f90 periodic_nbo/nbo.f90 +--- periodic_nbo.orig/nbo.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -1,6 +1,6 @@ + MODULE nbo + USE nbo_shared +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_nbo, output + +@@ -336,7 +336,7 @@ + !IF( jg /= ig )Pi = Pi - outer_product(bond_coeff(:,2*ibondorlp+1-inbo,jg),bond_coeff(:,2*ibondorlp+1-inbo,jg)) + !proj_dummy = P + !P = MATMUL(Pi,P) +- !CALL DGEMM_MKL95(Pi,proj_dummy,P,'N','N',1.d0,0.d0) ++ !CALL DGEMM(Pi,proj_dummy,P,'N','N',1.d0,0.d0) + + rhoat=0.d0 + rhoat(iifirst:iilast,iifirst:iilast)=inp%rho0(ifirst:ilast,ifirst:ilast,ig,ispin) +@@ -379,8 +379,8 @@ + + !Now project out all of the bonding and antibonding density, to leave solely the dentisy associated with Rydberg states + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- !CALL DGEMM_MKL95(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) +- !CALL DGEMM_MKL95(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) ++ !CALL DGEMM(inp%rho0(:,:,1),P,proj_dummy,'N','N',1.d0,0.d0) ++ !CALL DGEMM(P,proj_dummy,inp%rho0(:,:,1),'N','N',1.d0,0.d0) + + + !PRINT *, 'made it to doing rydberg search' +@@ -552,7 +552,7 @@ + Pi=Pi-outer_product(lpcontrib,lpcontrib) + Pdummy=P + !P=MATMUL(Pi,P) +- CALL DGEMM_MKL95(Pi,Pdummy,P,'N','N',1.d0,0.d0) ++ CALL DGEMM(Pi,Pdummy,P,'N','N',1.d0,0.d0) + + !IF( occ > core_thresh*DBLE(3-inp%nspins) )THEN + ! PRINT *, 'Removing CR from atom',iatom +@@ -563,8 +563,8 @@ + !PRINT * + + !inp%rho0(:,:,1) = MATMUL(P,(MATMUL(inp%rho0(:,:,1),P))) +- CALL DGEMM_MKL95(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) +- CALL DGEMM_MKL95(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) ++ CALL DGEMM(inp%rho0(:,:,1,ispin),P,Pdummy,'N','N',1.d0,0.d0) ++ CALL DGEMM(P,Pdummy,inp%rho0(:,:,1,ispin),'N','N',1.d0,0.d0) + + + END SUBROUTINE do_1c_search +@@ -966,7 +966,7 @@ + + FUNCTION schmidt_orthog_matrix(S,n) RESULT(Os) + USE matutil +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:) :: S + REAL*8,DIMENSION(n,n) :: Sinv +@@ -981,7 +981,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL DGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) ++ CALL DGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',1.d0,0.d0) + + !Now do gs orthogonalization using those projections + Os=0.d0 +diff -ru periodic_nbo.orig/nbo_shared.f90 periodic_nbo/nbo_shared.f90 +--- periodic_nbo.orig/nbo_shared.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/nbo_shared.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -151,7 +151,7 @@ + !Calculates the number of electrons in the unit cell + ! + SUBROUTINE calc_nelec(inp,is_orthog) +- USE MKL95_BLAS ++ USE BLAS95 + USE matutil + IMPLICIT NONE + TYPE(nbo_input) :: inp +@@ -167,9 +167,9 @@ + + DO ispin=1,inp%nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%sk(:,:,ik),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nelec=nelec+inp%kpt_wt(ik)*mattrace(nelec_dummy) +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),nelec_dummy,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + nenergy=nenergy+inp%kpt_wt(ik)*mattrace(nelec_dummy) + ENDDO + ENDDO +diff -ru periodic_nbo.orig/periodic_matutil.f90 periodic_nbo/periodic_matutil.f90 +--- periodic_nbo.orig/periodic_matutil.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/periodic_matutil.f90 2016-05-12 09:55:32.463039731 +0200 +@@ -41,7 +41,7 @@ + !Multiples two periodic matrices. + ! + FUNCTION periodic_matmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a,b + REAL*8,DIMENSION(SIZE(a,1),SIZE(a,2),SIZE(a,3)) :: c +@@ -101,7 +101,7 @@ + !$OMP END CRITICAL + IF (idg.GT.0.AND.normab.GT.thresh) THEN + ! c(:,:,ig)=c(:,:,ig)+MATMUL(a(:,:,igp),b(:,:,idg)) +- CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + !$OMP CRITICAL + imul=imul+1 + !$OMP END CRITICAL +@@ -118,7 +118,7 @@ + END FUNCTION periodic_matmul + + FUNCTION periodic_matvecmul(a,b) RESULT(c) +- USE MKL95_BLAS ++ USE BLAS95 + IMPLICIT NONE + REAL*8,DIMENSION(:,:,:), INTENT(in) :: a + REAL*8,DIMENSION(:,:), INTENT(IN) :: b +@@ -165,7 +165,7 @@ + IF (idg.GT.0) THEN + !WRITE(6,*)'non zero matrix',idg,indexg(:,idg) + c(:,ig)=c(:,ig)+MATMUL(a(:,:,idg),b(:,igp)) +- !CALL DGEMM_MKL95(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) ++ !CALL DGEMM(a(:,:,igp),b(:,:,idg),c(:,:,ig),'N','N',1.d0,1.d0) + imul=imul+1 + ENDIF + +diff -ru periodic_nbo.orig/pre_nao.f90 periodic_nbo/pre_nao.f90 +--- periodic_nbo.orig/pre_nao.f90 2015-03-04 18:06:25.000000000 +0100 ++++ periodic_nbo/pre_nao.f90 2016-05-12 10:18:03.939451000 +0200 +@@ -1,5 +1,5 @@ + MODULE pre_nao +- USE MKL95_BLAS ++ USE BLAS95 + PRIVATE + PUBLIC :: do_pre_nao + +@@ -18,7 +18,7 @@ + USE matutil + USE periodic_matutil + USE nbo_shared +- USE mkl95_LAPACK ++ USE LAPACK95 + IMPLICIT NONE + + TYPE(nbo_input) :: inp +@@ -135,9 +135,9 @@ + num_elec = 0.d0 + DO ispin=1,nspins + DO ik=1,nk +- CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(inp%rhok(:,:,ik,ispin),inp%fockk(:,:,ik,ispin),energy_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + energy_sum = energy_sum + inp%kpt_wt(ik)*mattrace(energy_test) +- !CALL ZGEMM_MKL95(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ !CALL ZGEMM(inp%rhok(:,:,ik,ispin),sk(:,:,ik),elec_test,'N','C',(1.d0,0.d0),(0.d0,0.d0)) + num_elec = num_elec + inp%kpt_wt(ik)*mattrace(inp%rhok(:,:,ik,ispin)) !sk should be the identity matrix now + ENDDO + ENDDO +@@ -193,8 +193,8 @@ + !$OMP PARALLEL DEFAULT(PRIVATE) SHARED(nk,rhok,sk) + !$OMP DO SCHEDULE(STATIC) + DO ik=1,nk +- CALL ZGEMM_MKL95(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL zGEMM_MKL95(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(rhok(:,:,ik),sk(:,:,ik),dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL zGEMM(sk(:,:,ik),dummy,rhok(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -298,7 +298,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),TRANSPOSE(N)) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),TRANSPOSE(N)) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(N,dummy,idenk(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + !$OMP END DO NOWAIT + !$OMP END PARALLEL +@@ -365,7 +365,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Step 3c: Restoration of natural character of NRB + !(Omitted; doesn't seem important at all) +@@ -451,7 +451,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'hi occ ryd orthog' + +@@ -461,7 +461,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Finally with the low occupancy NRB + !Here we first do a Gram-Schmidt orthogonalization of the low occupancy states to the remainder +@@ -469,7 +469,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Os) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Os) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Os,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !WRITE(6,*)'lo occ ryd orthog' + +@@ -480,7 +480,7 @@ + sk(:,:,ik)=matunitary_trans(sk(:,:,ik),Ow) + rhok(:,:,ik)=matunitary_trans(rhok(:,:,ik),Ow) + dummy = idenk(:,:,ik) +- CALL ZGEMM_MKL95(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Ow,dummy,idenk(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now restore the expected order of the basis functions + sk(:,:,ik)=remap_matrix(sk(:,:,ik),irydbasisremap,.TRUE.) +@@ -656,7 +656,7 @@ + !onto the remaining basis function n+1:nbasis + Sinv=matinv(S(1:n,1:n)) + !proj=MATMUL(Sinv,S(1:n,n+1:nbasis)) +- CALL ZGEMM_MKL95(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(Sinv,S(1:n,n+1:nbasis),proj,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Now do gs orthogonalization using those projections + Os=0.d0 +@@ -707,7 +707,7 @@ + nbasis=SIZE(N,1) + IF (PRESENT(S)) THEN + !overlap=MATMUL(matsqrt(S),N) +- CALL DGEMM_MKL95(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) ++ CALL DGEMM(matsqrt(S),N,overlap,'N','N',1.d0,0.d0) + ELSE + overlap=N + ENDIF diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO.eb new file mode 100644 index 0000000000..c629f66838 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'NBO' +version = '1.1' + +homepage = 'http://schmidt.chem.wisc.edu/nbosoftware' +description = """Generalized Natural Bond Orbital algorithm to handle systems characterized by periodic symmetry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] +sources = ['periodic_nbo_v.%(version)s.tgz'] + +patches = ['NBO-%(version)s_MKL95.patch'] + +buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' +buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' + +files_to_copy = [(['nbo.exe'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/nbo.exe'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From e6233dc104ac2488f8a7ea35ec3f5df51f8de4c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 11:10:16 +0200 Subject: [PATCH 0826/2403] fix filename of NBO easyconfig --- easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/NBO/{NBO.eb => NBO-1.1-intel-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/n/NBO/NBO.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/n/NBO/NBO.eb rename to easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb -- GitLab From 36481d302c326fb888f18395e9485de0369211c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 11:42:34 +0200 Subject: [PATCH 0827/2403] remove hack in HPL pomkl easyconfig for linking with -ldl --- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb index 7d18ed0de8..4d48990b54 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -15,9 +15,4 @@ source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] -# needs to include -ldl or else we get -# .../libmkl_core.a(mkl_memory_patched.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' -import os -os.environ['LIBS'] = '-ldl' - moduleclass = 'tools' -- GitLab From daf6705c34074fd88288abd68b8d470ffb390e3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 14:29:59 +0200 Subject: [PATCH 0828/2403] also build projection.exe tool in NBO easyconfig --- .../easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb | 18 +- .../n/NBO/projection-1.1.2_MKL95.patch | 212 ++++++++++++++++++ 2 files changed, 226 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch diff --git a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb index c629f66838..a0ff978b52 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-1.1-intel-2016a.eb @@ -10,17 +10,27 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'openmp': True} source_urls = ['http://schmidt.chem.wisc.edu/sites/schmidt.chem.wisc.edu/files/'] -sources = ['periodic_nbo_v.%(version)s.tgz'] +sources = [ + 'periodic_nbo_v.%(version)s.tgz', + 'projection_v.1.1.2.tgz', +] -patches = ['NBO-%(version)s_MKL95.patch'] +patches = [ + 'NBO-%(version)s_MKL95.patch', + ('projection-1.1.2_MKL95.patch', '..'), +] + +prebuildopts = "cd %(builddir)s/projection && " +prebuildopts += 'make FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" && ' +prebuildopts += "cd %(builddir)s/periodic_nbo && " buildopts = 'FC="$FC" LD="$FC" FFLAGS="$FFLAGS -I$LAPACK_INC_DIR/intel64/ilp64" ' buildopts += 'LDFLAGS="$FFLAGS $LDFLAGS $LIBLAPACK -lmkl_blas95_ilp64 -lmkl_lapack95_ilp64"' -files_to_copy = [(['nbo.exe'], 'bin')] +files_to_copy = [(['%(builddir)s/periodic_nbo/nbo.exe', '%(builddir)s/projection/projection.exe'], 'bin')] sanity_check_paths = { - 'files': ['bin/nbo.exe'], + 'files': ['bin/nbo.exe', 'bin/projection.exe'], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch new file mode 100644 index 0000000000..f12e3ac7a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/projection-1.1.2_MKL95.patch @@ -0,0 +1,212 @@ +fix using BLAS95/LAPACK95 interface for recent Intel MKL versions +author: Kenneth Hoste (HPC-UGent) +diff -ru projection.orig/bloch_overlap.f90 projection/bloch_overlap.f90 +--- projection.orig/bloch_overlap.f90 2015-04-15 18:05:39.000000000 +0200 ++++ projection/bloch_overlap.f90 2016-05-12 13:58:53.000000000 +0200 +@@ -18,8 +18,8 @@ + ! Kudin and Scuseria, Chem. Phys. Lett.; 289, 611-616 (1998) + + SUBROUTINE bloch_space_overlap(AO_basis,index_l) +- USE mkl95_lapack +- USE mkl95_blas ++ USE LAPACK95 ++ USE BLAS95 + IMPLICIT NONE + + TYPE(AO_function), DIMENSION(:) :: AO_basis +@@ -189,9 +189,9 @@ + bloch_s_inv(:,:,ik) = bloch_s_mat(:,:,ik) + IF( SVD )THEN + !SVD inversion method, more robust but slow +- CALL ZGESVD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') ++ CALL ZGESVD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,work_array,'A') + !Previously used SVD routine, has numerical instability wrt really small values +- !CALL ZGESDD_MKL95(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') ++ !CALL ZGESDD(bloch_s_inv(:,:,ik),sing_value,u_matrix,v_matrix,'A') + + !This loop is the equivalent of multiplying the inverse of the singular values matrix by adjoint of the u matrix + DO j=1,s_dim +@@ -202,16 +202,16 @@ + inv_dummy(j,:) = 0.d0 + ENDIF + ENDDO +- CALL ZGEMM_MKL95(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(v_matrix,inv_dummy,bloch_s_inv(:,:,ik),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + ELSE + !LU decompostion inversion method, fast but easily suffers from instability due to linear dependency +- CALL ZGETRF_MKL95(bloch_s_inv(:,:,ik),IPIV,INFO) ++ CALL ZGETRF(bloch_s_inv(:,:,ik),IPIV,INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The inverese of the overlap matrix for kpt',ik,'could not be computed' + WRITE(6,*)'INFO value output from ZGETRF',INFO + STOP + ENDIF +- CALL ZGETRI_MKL95(bloch_s_inv(:,:,ik),IPIV) ++ CALL ZGETRI(bloch_s_inv(:,:,ik),IPIV) + ENDIF + + !WRITE(6,*)'inverse for kpoint',ik +@@ -248,7 +248,7 @@ + !IF there are linear dependencies the best bet is to just 'trim' the basis set of its most diffuse functions. + !In periodic systems there is no 'edge' and these diffuse functions are largely uneccessary. + SUBROUTINE check_linear_depend(input_mat,eig_min) +- USE mkl95_lapack ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: input_mat +@@ -262,7 +262,7 @@ + + test_mat = input_mat + +- CALL ZHEEV_MKL95(test_mat,eigval,'V','U',INFO) ++ CALL ZHEEV(test_mat,eigval,'V','U',INFO) + + IF( INFO .NE. 0 )THEN + WRITE(6,*)'Calculating eigenvalues in check_linear_depend failed' +diff -ru projection.orig/projection_main.f90 projection/projection_main.f90 +--- projection.orig/projection_main.f90 2015-03-04 17:07:27.000000000 +0100 ++++ projection/projection_main.f90 2016-05-12 13:58:57.000000000 +0200 +@@ -4,7 +4,7 @@ + USE rd_basis + USE bloch_overlap + USE PAW +- USE mkl95_blas ++ USE BLAS95 + IMPLICIT NONE + + CHARACTER(128) :: basis_fn, VASP_fn, NBO_fn +@@ -145,28 +145,28 @@ + !Then for each basis function, nu, the contribution of the planewaves is calculated for all bands at one using vector-matrix multiplication + DO ispin=1,nspins + !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +- CALL ZGEMV_MKL95(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') ++ CALL ZGEMV(pw_coeff(:,:,ik,ispin),AO_PW_overlap(:,ik),proj_matrix(nu,:,ik,ispin),(1.d0,0.d0),(0.d0,0.d0),'T') + ENDDO + ENDDO + + DO ispin=1,nspins + ! !Calculation of planewave contributions to band coeff's are done at once using matrix multiplication + ! !each computation is SUM(nu) S-1{mu,nu} * (SUM(g) *c(a,g)) +-! CALL ZGEMM_MKL95(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(AO_PW_overlap(:,:,ik),pw_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ! + ! !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +-! IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++! IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + ! + ! !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + ! !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +-! CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++! CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + !Since band is simply summation of PW AND PAW, PAW contirbution is simply added to PW's +- IF( PAW_pseudo ) CALL ZGEMM_MKL95(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) ++ IF( PAW_pseudo ) CALL ZGEMM(PAW_overlap(:,:,ik),PAW_coeff(:,:,ik,ispin),proj_matrix(:,:,ik,ispin),'N','N',(1.d0,0.d0),(1.d0,0.d0)) + + !Band overlaps are finally multiplied by inverse of overlap matrix to complete projection + !The use of the inverse of the overlap matrix is necessary due to the non-orthogonality of the AO-basis +- CALL ZGEMM_MKL95(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_inv(:,:,ik),proj_matrix(:,:,ik,ispin),bloch_band_coeff(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + ENDDO + +@@ -208,19 +208,19 @@ + coeff_dummy(:,iband) = bloch_band_coeff(:,iband,ik,ispin) * weight(iband,ik,ispin) + ENDDO + !Matrix muliplication is used to calculate the density matrix +- CALL ZGEMM_MKL95(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,bloch_band_coeff(:,:,ik,ispin),bloch_density(:,:,ik,ispin),'N','C',(1.d0,0.d0),(0.d0,0.d0)) + + !FOCK MATRIX + !Matrix multiplication is used to convert the Fock matrix into the projected basis + ! F{mu,nu} = SUM(fock_coeff{nu,iband}*F{iband,iband}*CONJG(fock_coeff{nu,iband})) + !First the nonorthogonality of the bloch orbtials must be addressed since the MO->AO transform is not unitary + !coeff's must be multiplied by Overlap matrix +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),bloch_band_coeff(:,:,ik,ispin),coeff_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + !Then the trnsformation is simply a unitary transform using the new coefficients + DO iband=1,nbands + fock_dummy(iband,:) = eig(iband,ik,ispin)*CONJG(coeff_dummy(:,iband)) + ENDDO +- CALL ZGEMM_MKL95(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,fock_dummy,bloch_fock(:,:,ik,ispin),'N','N',(1.d0,0.d0),(0.d0,0.d0)) + ENDDO + ENDDO + +@@ -235,12 +235,12 @@ + energy_sum = 0.d0 + DO ispin=1,nspins + DO ik=1,nkpts +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_s_mat(:,:,ik),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + num_elec = num_elec + n_elec_dummy(nu,nu) + ENDDO +- CALL ZGEMM_MKL95(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_density(:,:,ik,ispin),bloch_fock(:,:,ik,ispin),n_elec_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + n_elec_dummy = n_elec_dummy*kpt_wt(ik) + DO nu=1,s_dim + energy_sum = energy_sum + n_elec_dummy(nu,nu) +@@ -271,7 +271,7 @@ + !This subrotuine computes the overlap matrices of the projected bands in the AO basis. + !This information is also used to calculate the spillover (quantify how much of band density is lost in projection + SUBROUTINE calc_spillover(r_mat,band_coeff) +- USE mkl95_blas ++ USE BLAS95 + USE rd_wavefunction + USE projection_shared + IMPLICIT NONE +@@ -345,8 +345,8 @@ + + !Overlap of projected bands is computed using matrix mulitplication + !Each overlap is equal to SUM(mu) SUM(nu) c*S{mu,nu}c +- CALL ZGEMM_MKL95(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) +- CALL ZGEMM_MKL95(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(bloch_s_mat(:,:,ik),band_coeff(:,:,ik,ispin),r_mat_dummy,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(band_coeff(:,:,ik,ispin),r_mat_dummy,r_mat(:,:,ik,ispin),'C','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !Then the norm of each band at each k-point is analyzed to make sure the norm is appropriate +diff -ru projection.orig/projection_shared.f90 projection/projection_shared.f90 +--- projection.orig/projection_shared.f90 2015-04-15 17:50:44.000000000 +0200 ++++ projection/projection_shared.f90 2016-05-12 13:59:00.000000000 +0200 +@@ -94,8 +94,8 @@ + !The bands are in the same original AO basis + !The orhtogonalizing matrix is constructed as W(WSW)^-1/2, where S is the 'overlap_mat' and W is a diagonal matrix containing the occupancy of each band + SUBROUTINE do_OWSO(overlap_mat,band_occ,band_coeff) +- USE mkl95_BLAS +- USE mkl95_LAPACK ++ USE BLAS95 ++ USE LAPACK95 + IMPLICIT NONE + + COMPLEX*16,DIMENSION(:,:),INTENT(IN) :: overlap_mat !Input overlap matrix, used to construct orthogonalizing matrix +@@ -145,7 +145,7 @@ + + !Now obtain the eigenvectors to obtain the square root matrix + eigvec = sym_weight +- CALL ZHEEV_MKL95(eigvec,eigval,'V','U',INFO) ++ CALL ZHEEV(eigvec,eigval,'V','U',INFO) + IF( INFO /= 0 )THEN + WRITE(6,*)'The eigenvalues of the overlap matrix could not be computed' + WRITE(6,*)'INFO on exit of ZHEEV',INFO +@@ -156,7 +156,7 @@ + DO iband=1,nbands + sym_weight(iband,:) = CONJG(eigvec(:,iband)) / SQRT(eigval(iband)) !Sym_weight is now just a dummy matrix for use in the BLAS routine + ENDDO +- CALL ZGEMM_MKL95(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(eigvec,sym_weight,sqrt_inv,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + !To obtain the orthogonlaizing matrix an additional multiplication by the weight matrix must be applied from the left +@@ -168,7 +168,7 @@ + !Now the bands can finally be orhtogonalized + !Note that the original coefficients are lost. They are currently unused but this will have to be rewritten if they become necessary. + coeff_dummy = band_coeff +- CALL ZGEMM_MKL95(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) ++ CALL ZGEMM(coeff_dummy,sqrt_inv,band_coeff,'N','N',(1.d0,0.d0),(0.d0,0.d0)) + + + -- GitLab From 81cb6797e4686ceaf9b0606870cce5f4518fd9ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 17:41:26 +0200 Subject: [PATCH 0829/2403] add easyconfig CheMPS2-1.7-rc2-intel-2016a.eb --- .../c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb new file mode 100644 index 0000000000..a6d4195a03 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.7-rc2' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('GSL', '2.1'), + ('HDF5', '1.8.16') +] + +buildopts = 'VERBOSE=1' + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' -- GitLab From a7c1b9ba4615973a4383146119a9f64f90dadea6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2016 17:44:43 +0200 Subject: [PATCH 0830/2403] remove VERBOSE=1 from buildopts for CheMPS2 --- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb | 2 -- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb index aab739ed19..c318ed2f59 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.6-intel-2016a.eb @@ -19,8 +19,6 @@ dependencies = [ ('HDF5', '1.8.16') ] -buildopts = 'VERBOSE=1' - runtest = 'test' separate_build_dir = True diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb index a6d4195a03..d7f97d6e59 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7-rc2-intel-2016a.eb @@ -19,8 +19,6 @@ dependencies = [ ('HDF5', '1.8.16') ] -buildopts = 'VERBOSE=1' - runtest = 'test' separate_build_dir = True -- GitLab From eaf991faae5eecdef7bd8c7e67741ad667cd6515 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 12:28:10 -0400 Subject: [PATCH 0831/2403] add VTK and SuiteSparse easyconfig it are necessary for fluid coupling module in yade, improve Yade easyconfig (sanity-check) --- ...uiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb | 27 +++++++++++ .../VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb | 48 +++++++++++++++++++ .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 30 +++++++----- 3 files changed, 93 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..69daf4f59c --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,27 @@ +name = 'SuiteSparse' +version = '4.5.2' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preconfigopts += 'LAPACK="$LIBLAPACK" ' +prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +prebuildopts += 'LAPACK="$LIBLAPACK" ' +preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' +preinstallopts += 'LAPACK="$LIBLAPACK" ' + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..e96c03e7a3 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('Python', '2.7.11'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libXt', '1.1.5'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 6ca7251d44..74cf92bc23 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -17,33 +17,39 @@ sources = [SOURCELOWER_TAR_GZ] mesaver = '11.2.1' dependencies = [ - ('Loki', '0.1.7'), ('Boost', '1.60.0', versionsuffix), + ('CGAL', '4.8', versionsuffix), + ('Eigen', '3.2.7'), + ('GDB', '7.10.1', versionsuffix), ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), - ('Python', '2.7.11'), + ('GTS', '0.7.6'), ('IPython', '3.2.3', versionsuffix), - ('PyGTS', '0.3.1', versionsuffix), - ('Eigen', '3.2.7'), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.1', versionsuffix), ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('GTS', '0.7.6'), - ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), - ('zlib', '1.2.8'), - ('CGAL', '4.8', versionsuffix), + ('SQLite', '3.9.2'), + ('SuiteSparse', '4.5.2', '-METIS-5.1.0'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), ] builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF -DENABLE_VTK=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts = '-DENABLE_GUI=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', - 'lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT], - 'dirs': ['lib/x86_64-linux-gnu/yade-%(version)s/py/yade'], + 'files': [('bin/yade-%(version)s', 'bin/yade-%(version)s-batch'), + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } moduleclass = 'devel' -- GitLab From d4c24166c7296977a365409e36ffbab0e5f1bd80 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 12 May 2016 18:30:42 +0200 Subject: [PATCH 0832/2403] Update SuiteSparse EasyConfig files after update of the EasyBlock --- .../SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb | 4 ---- .../SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb index ac231b59ef..be2d19e2ca 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-intel-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' - maxparallel = 1 moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb index 63fe3bdb3b..8f26d75a93 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-intel-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' - maxparallel = 1 moduleclass = 'numlib' -- GitLab From b9f2c26ddab0d6ceb7aaa7769e17fa5e8e902fa2 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 12:32:35 -0400 Subject: [PATCH 0833/2403] fix santy_check_paths --- .../easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 74cf92bc23..771c1391cd 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -46,7 +46,7 @@ configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' sanity_check_paths = { - 'files': [('bin/yade-%(version)s', 'bin/yade-%(version)s-batch'), + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], -- GitLab From 14c7469bfad8a9e8a5db7bf1415794928f835e16 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 13:28:27 -0400 Subject: [PATCH 0834/2403] add matplotlib-freetype-2.6.3 easyconfig to resolve conflict dependencies --- ...foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 44 +++++++++++++++++++ .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb new file mode 100644 index 0000000000..d74aeaeeca --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s-freetype-2.6.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.3'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 771c1391cd..3ae713b3be 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ dependencies = [ ('IPython', '3.2.3', versionsuffix), ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), ('Loki', '0.1.7'), - ('matplotlib', '1.5.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), ('minieigen', '0.5.3', versionsuffix), ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), -- GitLab From e7c51d2166ef05e976a4be67fae383e22298f09f Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 14:26:52 -0400 Subject: [PATCH 0835/2403] avoid hardcoding the freetype version in two places --- ...plotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index d74aeaeeca..528d8a13cb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -2,7 +2,6 @@ easyblock = 'Bundle' name = 'matplotlib' version = '1.5.1' -versionsuffix = '-Python-%(pyver)s-freetype-2.6.3' homepage = 'http://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of @@ -14,9 +13,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' +freetype_ver = '2.6.3' +versionsuffix = '-Python-%%(pyver)s-freetype-%s' % freetype_ver + dependencies = [ ('Python', '2.7.11'), - ('freetype', '2.6.3'), + ('freetype', freetype_ver), ('libpng', '1.6.21'), ] -- GitLab From e13db3b9bef67a50ea0f1c44236caa20592eb199 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 16:07:16 -0400 Subject: [PATCH 0836/2403] improve matplotlib and remove SuiteSparse easyconfig --- ...foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 1 + ...uiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb | 27 ------------------- .../Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 5 ++-- 3 files changed, 3 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 528d8a13cb..c9dd3410c4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -30,6 +30,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb deleted file mode 100644 index 69daf4f59c..0000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'SuiteSparse' -version = '4.5.2' - -homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} - -source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] -sources = [SOURCE_TAR_GZ] - -metis = 'METIS' -metis_ver = '5.1.0' -versionsuffix = '-%s-%s' % (metis, metis_ver) -dependencies = [(metis, metis_ver)] - -preconfigopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preconfigopts += 'LAPACK="$LIBLAPACK" ' -prebuildopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -prebuildopts += 'LAPACK="$LIBLAPACK" ' -preinstallopts = 'MY_METIS_LIB="$EBROOTMETIS/lib/libmetis.so" ' -preinstallopts += 'LAPACK="$LIBLAPACK" ' - -maxparallel = 1 - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index 3ae713b3be..dfcea93ba1 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -31,8 +31,7 @@ dependencies = [ ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('SQLite', '3.9.2'), - ('SuiteSparse', '4.5.2', '-METIS-5.1.0'), + ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), ] @@ -41,7 +40,7 @@ builddependencies = [('CMake', '3.5.2')] separate_build_dir = True -configopts = '-DENABLE_GUI=OFF ' +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' -- GitLab From 4742855b22f00d063e0c39a9334340a2c6f0b699 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Thu, 12 May 2016 16:50:22 -0400 Subject: [PATCH 0837/2403] add modextrapaths in Yade easyconfig --- .../y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index dfcea93ba1..f94f281e77 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -44,6 +44,12 @@ configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + sanity_check_paths = { 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, -- GitLab From 0d740a9f0879dc7e077305bef87a3a479c4e8eda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 11:00:37 +0200 Subject: [PATCH 0838/2403] use %(pyshortver)s rather than hardcoding 2.7 in VTK easyconfigs --- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb index 4be27d99f6..94b031902b 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb @@ -48,7 +48,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%s.%s " % (pyshortver, SHLIB_EXT) configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%s " % pyshortver -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%%(installdir)s/lib/python%s/site-packages:$PYTHONPATH && " % pyshortver modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index 55d38284a0..e549b2e963 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -43,7 +43,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From 071a61763eb77f420ab71153d85c722f878b8ede Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 13 May 2016 12:37:09 +0200 Subject: [PATCH 0839/2403] remove pre*=LAPACK="$LIBLAPACK" option --- .../s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb index 7b07d451fc..6a80824b3c 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'LAPACK="$LIBLAPACK" ' -prebuildopts = 'LAPACK="$LIBLAPACK" ' -preinstallopts = 'LAPACK="$LIBLAPACK" ' - maxparallel = 1 moduleclass = 'numlib' -- GitLab From a732161e4dce6dec6b86026064ac2bb30707e9f7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 13 May 2016 12:54:06 +0200 Subject: [PATCH 0840/2403] try to patch --- easybuild/easyconfigs/r/RSEM/Makefile | 173 +++++++ easybuild/easyconfigs/r/RSEM/Makefile.orig | 173 +++++++ .../r/RSEM/RSEM-1.2.30-foss-2016a.eb | 57 +++ .../r/RSEM/RSEM-1.2.30_boost.patch | 23 + .../r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch | 162 +++++++ easybuild/easyconfigs/r/RSEM/sam/Makefile | 314 +++++++++++++ .../easyconfigs/r/RSEM/sam/Makefile.orig | 314 +++++++++++++ easybuild/easyconfigs/r/RSEM/sam/diff | 23 + easybuild/easyconfigs/r/RSEM/sam/hts/Makefile | 426 ++++++++++++++++++ .../easyconfigs/r/RSEM/sam/hts/Makefile.orig | 426 ++++++++++++++++++ easybuild/easyconfigs/r/RSEM/sam/hts/diff | 18 + 11 files changed, 2109 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEM/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch create mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/sam/diff create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig create mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/diff diff --git a/easybuild/easyconfigs/r/RSEM/Makefile b/easybuild/easyconfigs/r/RSEM/Makefile new file mode 100644 index 0000000000..921b40b1b3 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/Makefile @@ -0,0 +1,173 @@ +SAMTOOLS = samtools-1.3 +HTSLIB = htslib-1.3 + +ifneq ($(cygwin), true) + SAMTOOLS_MAKEFILE = Makefile +else + SAMTOOLS_MAKEFILE = Makefile.cygwin +endif + +# overridable, defaulting to local copy +BOOST = ${EBROOTBOOST} + +# Compilation variables +CXX = g++ +CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +CPPFLAGS = + +LDFLAGS = +LDLIBS = + +# Installation variables +INSTALL = install +INSTALL_PROGRAM = $(INSTALL) -p +INSTALL_DATA = $(INSTALL) -p -m 644 +INSTALL_DIR = $(INSTALL) -d +STRIP ?=strip + +prefix ?= /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin + +# Auxiliary variables for compilation +SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h +SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a +CONFIGURE = ./configure + +OBJS1 = parseIt.o +OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o +OBJS3 = EM.o Gibbs.o calcCI.o simulation.o + +PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads +PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads +PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals + +PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) + +# Auxiliary variables for installation +SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ + rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ + extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem + + + + +.PHONY : all ebseq clean + +all : $(PROGRAMS) $(SAMTOOLS)/samtools + +$(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +$(SAMLIBS) : $(SAMTOOLS)/samtools + + +# Compile objects +$(OBJS1) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< + +$(OBJS2) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< + +$(OBJS3) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< + + +# Generate executables +$(PROGS1) : + $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) + +$(PROGS2) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -L$(EBROOTZLIB)/lib -lz + +$(PROGS3) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) + + +# Dependencies for executables +rsem-extract-reference-transcripts : extractRef.o +rsem-synthesis-reference-transcripts : synthesisRef.o +rsem-preref : preRef.o +rsem-build-read-index : buildReadIndex.o +rsem-simulate-reads : simulation.o + +rsem-parse-alignments : parseIt.o $(SAMLIBS) +rsem-run-em : EM.o SamHeader.o $(SAMLIBS) +rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) +rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) +rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) +rsem-get-unique : getUnique.o $(SAMLIBS) +rsem-sam-validator : samValidator.o $(SAMLIBS) +rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) + +rsem-run-gibbs : Gibbs.o +rsem-calculate-credibility-intervals : calcCI.o $(LDLIBS) + +# Dependencies for objects +parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h + +extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h +synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h +preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h +buildReadIndex.o : buildReadIndex.cpp utils.h +wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h +tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h +bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h +bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h +getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h +samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp + +EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h +Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h +calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h +simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h + +# Dependencies for header files +Transcript.h : utils.h +Transcripts.h : utils.h my_assert.h Transcript.h +BowtieRefSeqPolicy.h : RefSeqPolicy.h +RefSeq.h : utils.h +Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h +SingleRead.h : Read.h +SingleReadQ.h : Read.h +PairedEndRead.h : Read.h SingleRead.h +PairedEndReadQ.h : Read.h SingleReadQ.h +PairedEndHit.h : SingleHit.h +HitContainer.h : GroupInfo.h +sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h +SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h +simul.h : $(BOOST)/boost/random.hpp +ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h +SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h +SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h +PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h +PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h +HitWrapper.h : HitContainer.h +BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h +sampling.h : $(BOOST)/boost/random.hpp +WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h +bc_aux.h : $(SAMHEADERS) +BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h +Buffer.h : my_assert.h +SamHeader.hpp : $(SAMHEADERS) + +# Compile EBSeq +ebseq : + cd EBSeq && $(MAKE) all + +# Install RSEM +install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) + $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + +# Clean +clean : + rm -f *.o *~ $(PROGRAMS) + cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/Makefile.orig b/easybuild/easyconfigs/r/RSEM/Makefile.orig new file mode 100644 index 0000000000..09d2223b23 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/Makefile.orig @@ -0,0 +1,173 @@ +SAMTOOLS = samtools-1.3 +HTSLIB = htslib-1.3 + +ifneq ($(cygwin), true) + SAMTOOLS_MAKEFILE = Makefile +else + SAMTOOLS_MAKEFILE = Makefile.cygwin +endif + +# overridable, defaulting to local copy +BOOST = . + +# Compilation variables +CXX = g++ +CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +CPPFLAGS = + +LDFLAGS = +LDLIBS = + +# Installation variables +INSTALL = install +INSTALL_PROGRAM = $(INSTALL) -p +INSTALL_DATA = $(INSTALL) -p -m 644 +INSTALL_DIR = $(INSTALL) -d +STRIP ?=strip + +prefix ?= /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin + +# Auxiliary variables for compilation +SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h +SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a +CONFIGURE = ./configure + +OBJS1 = parseIt.o +OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o +OBJS3 = EM.o Gibbs.o calcCI.o simulation.o + +PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads +PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads +PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals + +PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) + +# Auxiliary variables for installation +SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ + rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ + extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem + + + + +.PHONY : all ebseq clean + +all : $(PROGRAMS) $(SAMTOOLS)/samtools + +$(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +$(SAMLIBS) : $(SAMTOOLS)/samtools + + +# Compile objects +$(OBJS1) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< + +$(OBJS2) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< + +$(OBJS3) : + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< + + +# Generate executables +$(PROGS1) : + $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) + +$(PROGS2) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz + +$(PROGS3) : + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) + + +# Dependencies for executables +rsem-extract-reference-transcripts : extractRef.o +rsem-synthesis-reference-transcripts : synthesisRef.o +rsem-preref : preRef.o +rsem-build-read-index : buildReadIndex.o +rsem-simulate-reads : simulation.o + +rsem-parse-alignments : parseIt.o $(SAMLIBS) +rsem-run-em : EM.o SamHeader.o $(SAMLIBS) +rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) +rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) +rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) +rsem-get-unique : getUnique.o $(SAMLIBS) +rsem-sam-validator : samValidator.o $(SAMLIBS) +rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) + +rsem-run-gibbs : Gibbs.o +rsem-calculate-credibility-intervals : calcCI.o + +# Dependencies for objects +parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h + +extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h +synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h +preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h +buildReadIndex.o : buildReadIndex.cpp utils.h +wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h +tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h +bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h +bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h +getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h +samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h +SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp + +EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h +Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h +calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h +simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h + +# Dependencies for header files +Transcript.h : utils.h +Transcripts.h : utils.h my_assert.h Transcript.h +BowtieRefSeqPolicy.h : RefSeqPolicy.h +RefSeq.h : utils.h +Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h +SingleRead.h : Read.h +SingleReadQ.h : Read.h +PairedEndRead.h : Read.h SingleRead.h +PairedEndReadQ.h : Read.h SingleReadQ.h +PairedEndHit.h : SingleHit.h +HitContainer.h : GroupInfo.h +sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h +SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h +simul.h : $(BOOST)/boost/random.hpp +ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h +SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h +SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h +PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h +PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h +HitWrapper.h : HitContainer.h +BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h +sampling.h : $(BOOST)/boost/random.hpp +WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h +bc_aux.h : $(SAMHEADERS) +BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h +Buffer.h : my_assert.h +SamHeader.hpp : $(SAMHEADERS) + +# Compile EBSeq +ebseq : + cd EBSeq && $(MAKE) all + +# Install RSEM +install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) + $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + +# Clean +clean : + rm -f *.o *~ $(PROGRAMS) + cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb new file mode 100644 index 0000000000..0daeb572d1 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -0,0 +1,57 @@ +easyblock = 'MakeCp' + +name = 'RSEM' +version = '1.2.30' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +#patches = ['RSEM-%(version)s_boost.patch'] + +dependencies = [ + ('ncurses', '6.0'), +] + +list_of_executables = [ + "rsem_perl_utils.pm", + "rsem-bam2readdepth", + "rsem-bam2wig", + "rsem-build-read-index", + "rsem-calculate-credibility-intervals", + "rsem-calculate-expression", + "rsem-control-fdr", + "rsem-extract-reference-transcripts", + "rsem-generate-data-matrix", + "rsem-generate-ngvector", + "rsem-gen-transcript-plots", + "rsem-get-unique", + "rsem-gff3-to-gtf", + "rsem-parse-alignments", + "rsem-plot-model", + "rsem-plot-transcript-wiggles", + "rsem-prepare-reference", + "rsem-preref", + "rsem-refseq-extract-primary-assembly", + "rsem-run-ebseq", + "rsem-run-em", + "rsem-run-gibbs", + "rsem-sam-validator", + "rsem-scan-for-paired-end-reads", + "rsem-simulate-reads", + "rsem-synthesis-reference-transcripts", + "rsem-tbam2gbam", +] + +files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] + +sanity_check_paths = { + 'files': ['''"bin/%s" % x for x in list_of_executables'''], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch new file mode 100644 index 0000000000..5782cb6a2d --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch @@ -0,0 +1,23 @@ +--- samtools-1.3/Makefile.orig 2016-05-13 11:39:28.000000000 +0200 ++++ samtools-1.3/Makefile 2016-05-13 11:42:52.000000000 +0200 +@@ -21,9 +21,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + CPPFLAGS = +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + LDFLAGS = + LIBS = + +@@ -83,7 +83,7 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch new file mode 100644 index 0000000000..206ac1fda2 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch @@ -0,0 +1,162 @@ +#Use EB provided libz and use EB provided CXX and CXXFLAGS +# January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) +--- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ Makefile 2016-01-18 12:02:56.406105229 +0100 +@@ -1,6 +1,6 @@ +-CC = g++ +-CFLAGS = -Wall -c -I. +-COFLAGS = -Wall -O3 -ffast-math -c -I. ++#CC = g++ ++#CFLAGS = -Wall -c -I. ++COFLAGS = ${CXXFLAGS} -Wall -c -I. + PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean +@@ -8,6 +8,8 @@ + all : $(PROGRAMS) + + sam/libbam.a : ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/Makefile ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/bcftools/Makefile + cd sam ; ${MAKE} all + + Transcript.h : utils.h +@@ -15,10 +17,10 @@ + Transcripts.h : utils.h my_assert.h Transcript.h + + rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp +- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} extractRef.cpp -o rsem-extract-reference-transcripts + + rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp +- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CXX) -Wall ${CXXFLAGS} synthesisRef.cpp -o rsem-synthesis-reference-transcripts + + BowtieRefSeqPolicy.h : RefSeqPolicy.h + +@@ -28,10 +30,10 @@ + + + rsem-preref : preRef.o +- $(CC) preRef.o -o rsem-preref ++ $(CXX) preRef.o -o rsem-preref + + preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp +- $(CC) $(COFLAGS) preRef.cpp ++ $(CXX) $(COFLAGS) preRef.cpp + + + SingleRead.h : Read.h +@@ -52,14 +54,14 @@ + + + rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++ $(CXX) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp +- $(CC) -Wall -O2 -c -I. parseIt.cpp ++ $(CXX) $(COFLAGS) parseIt.cpp + + + rsem-build-read-index : utils.h buildReadIndex.cpp +- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CXX) ${CXXFLAGS} buildReadIndex.cpp -o rsem-build-read-index + + + simul.h : boost/random.hpp +@@ -87,57 +89,57 @@ + WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h + + rsem-run-em : EM.o sam/libbam.a +- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread ++ $(CXX) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread + + EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp +- $(CC) $(COFLAGS) EM.cpp ++ $(CXX) $(COFLAGS) EM.cpp + + bc_aux.h : sam/bam.h + + BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h + + rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a +- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp +- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp +- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h +- $(CC) $(COFLAGS) wiggle.cpp ++ $(CXX) $(COFLAGS) wiggle.cpp + + rsem-simulate-reads : simulation.o +- $(CC) -o rsem-simulate-reads simulation.o ++ $(CXX) -o rsem-simulate-reads simulation.o + + simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp +- $(CC) $(COFLAGS) simulation.cpp ++ $(CXX) $(COFLAGS) simulation.cpp + + rsem-run-gibbs : Gibbs.o +- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread ++ $(CXX) -o rsem-run-gibbs Gibbs.o -lpthread + + #some header files are omitted + Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp +- $(CC) $(COFLAGS) Gibbs.cpp ++ $(CXX) $(COFLAGS) Gibbs.cpp + + Buffer.h : my_assert.h + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread ++ $(CXX) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + + #some header files are omitted + calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp +- $(CC) $(COFLAGS) calcCI.cpp ++ $(CXX) $(COFLAGS) calcCI.cpp + + rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a +- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a +- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a +- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CXX) ${CXXFLAGS} -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ + + ebseq : + cd EBSeq ; ${MAKE} all +--- sam/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 +@@ -1,7 +1,7 @@ +-CC= gcc ++#CC= gcc + CFLAGS_EXTRA= + #CFLAGS_EXTRA= -L/usr/include/ncurses +-CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) ++#CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib + DFLAGS_EXTRA= + #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log +--- sam/bcftools/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 ++++ sam/bcftools/Makefile 2016-01-18 12:09:10.076063429 +0100 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc ++#CC= gcc ++#CFLAGS= -g -Wall -O2 #-m64 #-arch ppc + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. \ No newline at end of file diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile b/easybuild/easyconfigs/r/RSEM/sam/Makefile new file mode 100644 index 0000000000..c7e392d67c --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/Makefile @@ -0,0 +1,314 @@ +# Makefile for samtools, utilities for the Sequence Alignment/Map format. +# +# Copyright (C) 2008-2015 Genome Research Ltd. +# Portions copyright (C) 2010-2012 Broad Institute. +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +#CC = gcc +CPPFLAGS = +#CFLAGS = -g -Wall -O2 +LDFLAGS = +LIBS = + +DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +AOBJS= bam_index.o bam_plcmd.o sam_view.o \ + bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ + bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ + bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + + +PROGRAMS = samtools + +BUILT_MISC_PROGRAMS = \ + misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ + misc/md5fa misc/md5sum-lite misc/wgsim + +MISC_PROGRAMS = \ + $(BUILT_MISC_PROGRAMS) \ + misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ + misc/interpolate_sam.pl misc/novo2sam.pl \ + misc/plot-bamstats misc/psl2sam.pl \ + misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ + misc/soap2sam.pl \ + misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl + +BUILT_TEST_PROGRAMS = \ + test/merge/test_bam_translate \ + test/merge/test_rtrans_build \ + test/merge/test_trans_tbl_init \ + test/split/test_count_rg \ + test/split/test_expand_format_string \ + test/split/test_filter_header_rg \ + test/split/test_parse_args \ + test/vcf-miniview + +all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + +# Usually config.mk and config.h are generated by running configure +# or config.status, but if those aren't used create defaults here. + +config.mk: + @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ + +config.h: + echo '/* Basic config.h generated by Makefile */' > $@ + echo '#define HAVE_CURSES' >> $@ + echo '#define HAVE_CURSES_H' >> $@ + +include config.mk + + +PACKAGE_VERSION = 1.3 + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, +# comment out this conditional. +ifneq "$(wildcard .git)" "" +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +# If you don't have GNU Make but are building from a Git repository, you may +# wish to replace this with a rule that always rebuilds version.h: +# version.h: force +# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ +version.h: + echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .c .o + +.c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + + +lib:libbam.a + +libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +samtools: $(AOBJS) libbam.a $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) + +bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h +bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +sam_h = sam.h $(htslib_sam_h) $(bam_h) +sam_opts_h = sam_opts.h $(htslib_hts_h) +sample_h = sample.h $(htslib_kstring_h) + +bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h +bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) +bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) +bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) +bam_aux.o: bam_aux.c $(bam_h) +bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) +bam_color.o: bam_color.c $(bam_h) +bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) +bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) +bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) +bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) +bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) +bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) +bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h +bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) +bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) +bam_tview_html.o: bam_tview_html.c $(bam_tview_h) +bam_flags.o: bam_flags.c $(htslib_sam_h) +bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) +dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +errmod.o: errmod.c errmod.h $(htslib_ksort_h) +kprobaln.o: kprobaln.c kprobaln.h +padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +sam.o: sam.c $(htslib_faidx_h) $(sam_h) +sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) +sam_opts.o: sam_opts.c $(sam_opts_h) +sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +sample.o: sample.c $(sample_h) $(htslib_khash_h) +stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) + + +# test programs + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +# (regression.sh sets $REF_PATH to a subdirectory itself.) +check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init + cd test/mpileup && ./regression.sh mpileup.reg + cd test/mpileup && ./regression.sh depth.reg + test/split/test_count_rg + test/split/test_expand_format_string + test/split/test_filter_header_rg + test/split/test_parse_args + + +test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + +test_test_h = test/test.h $(htslib_sam_h) + +test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) +test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o +test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o +test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) +test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) +test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) +test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) +test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) +test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) + + +# misc programs + +misc/ace2sam: misc/ace2sam.o + $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + +misc/maq2sam-short: misc/maq2sam-short.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + +misc/maq2sam-long: misc/maq2sam-long.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + +misc/md5fa: misc/md5fa.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) +misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) +misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) +misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) + +misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + +misc/maq2sam-long.o: misc/maq2sam.c + $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + + +install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) + $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) + + +testclean: + -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* + -cd test/dat && rm -f test_input_*.bam.bai + -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* + +mostlyclean: testclean + -rm -f *.o misc/*.o test/*.o test/*/*.o version.h + +clean: mostlyclean + -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +distclean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS + +clean-all: clean clean-htslib + + +tags: + ctags -f TAGS *.[ch] misc/*.[ch] + + +force: + + +.PHONY: all check clean clean-all distclean force install +.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig new file mode 100644 index 0000000000..525288c2c8 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig @@ -0,0 +1,314 @@ +# Makefile for samtools, utilities for the Sequence Alignment/Map format. +# +# Copyright (C) 2008-2015 Genome Research Ltd. +# Portions copyright (C) 2010-2012 Broad Institute. +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +CC = gcc +CPPFLAGS = +CFLAGS = -g -Wall -O2 +LDFLAGS = +LIBS = + +DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +AOBJS= bam_index.o bam_plcmd.o sam_view.o \ + bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ + bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ + bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + + +PROGRAMS = samtools + +BUILT_MISC_PROGRAMS = \ + misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ + misc/md5fa misc/md5sum-lite misc/wgsim + +MISC_PROGRAMS = \ + $(BUILT_MISC_PROGRAMS) \ + misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ + misc/interpolate_sam.pl misc/novo2sam.pl \ + misc/plot-bamstats misc/psl2sam.pl \ + misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ + misc/soap2sam.pl \ + misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl + +BUILT_TEST_PROGRAMS = \ + test/merge/test_bam_translate \ + test/merge/test_rtrans_build \ + test/merge/test_trans_tbl_init \ + test/split/test_count_rg \ + test/split/test_expand_format_string \ + test/split/test_filter_header_rg \ + test/split/test_parse_args \ + test/vcf-miniview + +all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally +ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +ALL_LIBS = -lz -ldl $(LIBS) + +# Usually config.mk and config.h are generated by running configure +# or config.status, but if those aren't used create defaults here. + +config.mk: + @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ + +config.h: + echo '/* Basic config.h generated by Makefile */' > $@ + echo '#define HAVE_CURSES' >> $@ + echo '#define HAVE_CURSES_H' >> $@ + +include config.mk + + +PACKAGE_VERSION = 1.3 + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, +# comment out this conditional. +ifneq "$(wildcard .git)" "" +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +# If you don't have GNU Make but are building from a Git repository, you may +# wish to replace this with a rule that always rebuilds version.h: +# version.h: force +# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ +version.h: + echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .c .o + +.c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + + +lib:libbam.a + +libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +samtools: $(AOBJS) libbam.a $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) + +bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h +bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +sam_h = sam.h $(htslib_sam_h) $(bam_h) +sam_opts_h = sam_opts.h $(htslib_hts_h) +sample_h = sample.h $(htslib_kstring_h) + +bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h +bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h +bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) +bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) +bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) +bam_aux.o: bam_aux.c $(bam_h) +bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) +bam_color.o: bam_color.c $(bam_h) +bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) +bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) +bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) +bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) +bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) +bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) +bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) +bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) +bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h +bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) +bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) +bam_tview_html.o: bam_tview_html.c $(bam_tview_h) +bam_flags.o: bam_flags.c $(htslib_sam_h) +bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h +bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) +dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) +errmod.o: errmod.c errmod.h $(htslib_ksort_h) +kprobaln.o: kprobaln.c kprobaln.h +padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) +phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +sam.o: sam.c $(htslib_faidx_h) $(sam_h) +sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) +sam_opts.o: sam_opts.c $(sam_opts_h) +sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +sample.o: sample.c $(sample_h) $(htslib_khash_h) +stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) +stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) + + +# test programs + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +# (regression.sh sets $REF_PATH to a subdirectory itself.) +check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init + cd test/mpileup && ./regression.sh mpileup.reg + cd test/mpileup && ./regression.sh depth.reg + test/split/test_count_rg + test/split/test_expand_format_string + test/split/test_filter_header_rg + test/split/test_parse_args + + +test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + +test_test_h = test/test.h $(htslib_sam_h) + +test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) +test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o +test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o +test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) +test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) +test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) +test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) +test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) +test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) + + +# misc programs + +misc/ace2sam: misc/ace2sam.o + $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + +misc/maq2sam-short: misc/maq2sam-short.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + +misc/maq2sam-long: misc/maq2sam-long.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + +misc/md5fa: misc/md5fa.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) + +misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) +misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) +misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) +misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) + +misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + +misc/maq2sam-long.o: misc/maq2sam.c + $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c + + +install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) + $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) + + +testclean: + -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* + -cd test/dat && rm -f test_input_*.bam.bai + -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* + +mostlyclean: testclean + -rm -f *.o misc/*.o test/*.o test/*/*.o version.h + +clean: mostlyclean + -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) + +distclean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS + +clean-all: clean clean-htslib + + +tags: + ctags -f TAGS *.[ch] misc/*.[ch] + + +force: + + +.PHONY: all check clean clean-all distclean force install +.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/diff b/easybuild/easyconfigs/r/RSEM/sam/diff new file mode 100644 index 0000000000..2469cafcc9 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/diff @@ -0,0 +1,23 @@ +--- Makefile.orig 2016-05-13 11:39:28.000000000 +0200 ++++ Makefile 2016-05-13 12:29:50.000000000 +0200 +@@ -21,9 +21,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + CPPFLAGS = +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + LDFLAGS = + LIBS = + +@@ -83,7 +83,7 @@ + # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally + ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz -ldl $(LIBS) ++ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile new file mode 100644 index 0000000000..00c103599b --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile @@ -0,0 +1,426 @@ +# Makefile for htslib, a C library for high-throughput sequencing data formats. +# +# Copyright (C) 2013-2015 Genome Research Ltd. +# +# Author: John Marshall +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +#CC = gcc +AR = ar +RANLIB = ranlib + +CPPFLAGS = +# TODO: probably update cram code to make it compile cleanly with -Wc++-compat +#CFLAGS = -g -Wall -O2 +EXTRA_CFLAGS_PIC = -fpic +LDFLAGS = +LIBS = + +# For now these don't work too well as samtools also needs to know to +# add -lbz2 and -llzma if linking against the static libhts.a library. +# TODO This needs configury and adding to htslib.pc.in. +# +# # Bzip2 support; optionally used by CRAM. +# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBBZ2)" "yes" +# CPPFLAGS += -DHAVE_LIBBZ2 +# LIBS += -lbz2 +# endif +# +# # Lzma support; optionally used by CRAM. +# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBLZMA)" "yes" +# CPPFLAGS += -DHAVE_LIBLZMA +# LIBS += -llzma +# endif + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +includedir = $(prefix)/include +libdir = $(exec_prefix)/lib +libexecdir = $(exec_prefix)/libexec +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 +man5dir = $(mandir)/man5 +pkgconfigdir= $(libdir)/pkgconfig + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + +# Set by config.mk if plugins are enabled +plugindir = + +BUILT_PROGRAMS = \ + bgzip \ + htsfile \ + tabix + +BUILT_TEST_PROGRAMS = \ + test/fieldarith \ + test/hfile \ + test/sam \ + test/test-regidx \ + test/test_view \ + test/test-vcf-api \ + test/test-vcf-sweep + +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) + +HTSPREFIX = +include htslib_vars.mk + + +PACKAGE_VERSION = 1.3 +LIBHTS_SOVERSION = 1 + + +# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string +# even if this is a dirty or untagged Git working tree. +NUMERIC_VERSION = $(PACKAGE_VERSION) + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# Much of this is also GNU Make-specific. If you don't have GNU Make and/or +# are not building from a Git repository, comment out this conditional. +ifneq "$(wildcard .git)" "" +original_version := $(PACKAGE_VERSION) +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag +# with a numeric name, revert $(NUMERIC_VERSION) to the original version number +# written above, but with the patchlevel field bumped to 255. +ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." +empty := +NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) +endif + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +version.h: + echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .bundle .c .o .pico .so + +.c.o: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< + +.c.pico: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + +LIBHTS_OBJS = \ + kfunc.o \ + knetfile.o \ + kstring.o \ + bgzf.o \ + faidx.o \ + hfile.o \ + hfile_net.o \ + hts.o \ + md5.o \ + regidx.o \ + sam.o \ + synced_bcf_reader.o \ + vcf_sweep.o \ + tbx.o \ + vcf.o \ + vcfutils.o \ + cram/cram_codecs.o \ + cram/cram_decode.o \ + cram/cram_encode.o \ + cram/cram_external.o \ + cram/cram_index.o \ + cram/cram_io.o \ + cram/cram_samtools.o \ + cram/cram_stats.o \ + cram/files.o \ + cram/mFILE.o \ + cram/open_trace_file.o \ + cram/pooled_alloc.o \ + cram/rANS_static.o \ + cram/sam_header.o \ + cram/string_alloc.o \ + cram/thread_pool.o \ + cram/vlen.o \ + cram/zfio.o + +PLUGIN_OBJS = + +cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) +cram_io_h = cram/cram_io.h $(cram_misc_h) +cram_misc_h = cram/misc.h cram/os.h +cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) +cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) +cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) +cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h +hfile_internal_h = hfile_internal.h $(htslib_hfile_h) +hts_internal_h = hts_internal.h $(htslib_hts_h) + + +# To be effective, config.mk needs to appear after most Makefile variables are +# set but before most rules appear, so that it can both use previously-set +# variables in its own rules' prerequisites and also update variables for use +# in later rules' prerequisites. + +# If your make doesn't accept -include, change this to 'include' if you are +# using the configure script or just comment the line out if you are not. +-include config.mk + +# Usually config.h is generated by running configure or config.status, +# but if those aren't used create a default config.h here. +config.h: + echo '/* Empty config.h generated by Makefile */' > $@ + + +lib-static: libhts.a + +# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have +# GNU Make, comment out the parts of this conditional that don't apply. +PLATFORM := $(shell uname -s) +ifeq "$(PLATFORM)" "Darwin" +SHLIB_FLAVOUR = dylib +lib-shared: libhts.dylib +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) +else +SHLIB_FLAVOUR = so +lib-shared: libhts.so +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) +endif + +plugins: $(BUILT_PLUGINS) + + +libhts.a: $(LIBHTS_OBJS) + @-rm -f $@ + $(AR) -rc $@ $(LIBHTS_OBJS) + -$(RANLIB) $@ + + +# The target here is libhts.so, as that is the built file that other rules +# depend upon and that is used when -lhts appears in other program's recipes. +# As a byproduct invisible to make, libhts.so.NN is also created, as it is the +# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + +libhts.so: $(LIBHTS_OBJS:.o=.pico) + $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + +# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH +# includes this project's build directory). + +libhts.dylib: $(LIBHTS_OBJS) + $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + +.pico.so: + $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) + +.o.bundle: + $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) + + +bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) +kstring.o kstring.pico: kstring.c $(htslib_kstring_h) +knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) +hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) +hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) +hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) +vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) +sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) +tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) +faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) +synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) +vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) +vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) +kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) +regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) +md5.o md5.pico: md5.c config.h $(htslib_hts_h) +plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) + +cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) +cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) +cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) +cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) +cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) +cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h +cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) +cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h +cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) +cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h +cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h +cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h +cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h +cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h +cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h +cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h + + +bgzip: bgzip.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) + +htsfile: htsfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) + +tabix: tabix.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) + +bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) +htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) +tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) + + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +check test: htsfile $(BUILT_TEST_PROGRAMS) + test/fieldarith test/fieldarith.sam + test/hfile + test/sam test/ce.fa test/faidx.fa + test/test-regidx + cd test && REF_PATH=: ./test_view.pl + cd test && REF_PATH=: ./test.pl + +test/fieldarith: test/fieldarith.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) + +test/hfile: test/hfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) + +test/sam: test/sam.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) + +test/test-regidx: test/test-regidx.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) + +test/test_view: test/test_view.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) + +test/test-vcf-api: test/test-vcf-api.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) + +test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) + +test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) +test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) +test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) +test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) +test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) +test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) +test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) + + +install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig + $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) + if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi + $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib + $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a + $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) + $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) + +installdirs: + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) + if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi + +# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, +# with symlinks libhts.so (used via -lhts during linking of client programs) +# and libhts.so.NN (used by client executables at runtime). + +install-so: libhts.so installdirs + $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) + +install-dylib: libhts.dylib installdirs + $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib + +# Substitute these pseudo-autoconf variables only at install time +# so that "make install prefix=/prefix/path" etc continue to work. +install-pkgconfig: installdirs + sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc + chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc + +# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides +# flags for building against the uninstalled library in this build directory. +htslib-uninstalled.pc: htslib.pc.in + sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ + + +testclean: + -rm -f test/*.tmp test/*.tmp.* + +mostlyclean: testclean + -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h + +clean: mostlyclean clean-$(SHLIB_FLAVOUR) + -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) + +distclean maintainer-clean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS *-uninstalled.pc + +clean-so: + -rm -f libhts.so libhts.so.* + +clean-dylib: + -rm -f libhts.dylib libhts.*.dylib + + +tags TAGS: + ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h + +# We recommend libhts-using programs be built against a separate htslib +# installation. However if you feel that you must bundle htslib source +# code with your program, this hook enables Automake-style "make dist" +# for this subdirectory. If you do bundle an htslib snapshot, please +# add identifying information to $(PACKAGE_VERSION) as appropriate. +# (The wildcards attempt to omit non-exported files (.git*, README.md, +# etc) and other detritus that might be in the top-level directory.) +distdir: + tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) + +cd $(distdir) && $(MAKE) distclean + +force: + + +.PHONY: all check clean distclean distdir force +.PHONY: install install-pkgconfig installdirs lib-shared lib-static +.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean +.PHONY: clean-so install-so +.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig new file mode 100644 index 0000000000..be2405e71c --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig @@ -0,0 +1,426 @@ +# Makefile for htslib, a C library for high-throughput sequencing data formats. +# +# Copyright (C) 2013-2015 Genome Research Ltd. +# +# Author: John Marshall +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + +CC = gcc +AR = ar +RANLIB = ranlib + +CPPFLAGS = +# TODO: probably update cram code to make it compile cleanly with -Wc++-compat +CFLAGS = -g -Wall -O2 +EXTRA_CFLAGS_PIC = -fpic +LDFLAGS = +LIBS = + +# For now these don't work too well as samtools also needs to know to +# add -lbz2 and -llzma if linking against the static libhts.a library. +# TODO This needs configury and adding to htslib.pc.in. +# +# # Bzip2 support; optionally used by CRAM. +# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBBZ2)" "yes" +# CPPFLAGS += -DHAVE_LIBBZ2 +# LIBS += -lbz2 +# endif +# +# # Lzma support; optionally used by CRAM. +# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) +# ifeq "$(HAVE_LIBLZMA)" "yes" +# CPPFLAGS += -DHAVE_LIBLZMA +# LIBS += -llzma +# endif + +prefix = /usr/local +exec_prefix = $(prefix) +bindir = $(exec_prefix)/bin +includedir = $(prefix)/include +libdir = $(exec_prefix)/lib +libexecdir = $(exec_prefix)/libexec +datarootdir = $(prefix)/share +mandir = $(datarootdir)/man +man1dir = $(mandir)/man1 +man5dir = $(mandir)/man5 +pkgconfigdir= $(libdir)/pkgconfig + +MKDIR_P = mkdir -p +INSTALL = install -p +INSTALL_PROGRAM = $(INSTALL) +INSTALL_DATA = $(INSTALL) -m 644 +INSTALL_DIR = $(MKDIR_P) -m 755 + +# Set by config.mk if plugins are enabled +plugindir = + +BUILT_PROGRAMS = \ + bgzip \ + htsfile \ + tabix + +BUILT_TEST_PROGRAMS = \ + test/fieldarith \ + test/hfile \ + test/sam \ + test/test-regidx \ + test/test_view \ + test/test-vcf-api \ + test/test-vcf-sweep + +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) + +HTSPREFIX = +include htslib_vars.mk + + +PACKAGE_VERSION = 1.3 +LIBHTS_SOVERSION = 1 + + +# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string +# even if this is a dirty or untagged Git working tree. +NUMERIC_VERSION = $(PACKAGE_VERSION) + +# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git +# description of the working tree: either a release tag with the same value +# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. +# Much of this is also GNU Make-specific. If you don't have GNU Make and/or +# are not building from a Git repository, comment out this conditional. +ifneq "$(wildcard .git)" "" +original_version := $(PACKAGE_VERSION) +PACKAGE_VERSION := $(shell git describe --always --dirty) + +# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag +# with a numeric name, revert $(NUMERIC_VERSION) to the original version number +# written above, but with the patchlevel field bumped to 255. +ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." +empty := +NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) +endif + +# Force version.h to be remade if $(PACKAGE_VERSION) has changed. +version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) +endif + +version.h: + echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ + +print-version: + @echo $(PACKAGE_VERSION) + + +.SUFFIXES: .bundle .c .o .pico .so + +.c.o: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< + +.c.pico: + $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + +LIBHTS_OBJS = \ + kfunc.o \ + knetfile.o \ + kstring.o \ + bgzf.o \ + faidx.o \ + hfile.o \ + hfile_net.o \ + hts.o \ + md5.o \ + regidx.o \ + sam.o \ + synced_bcf_reader.o \ + vcf_sweep.o \ + tbx.o \ + vcf.o \ + vcfutils.o \ + cram/cram_codecs.o \ + cram/cram_decode.o \ + cram/cram_encode.o \ + cram/cram_external.o \ + cram/cram_index.o \ + cram/cram_io.o \ + cram/cram_samtools.o \ + cram/cram_stats.o \ + cram/files.o \ + cram/mFILE.o \ + cram/open_trace_file.o \ + cram/pooled_alloc.o \ + cram/rANS_static.o \ + cram/sam_header.o \ + cram/string_alloc.o \ + cram/thread_pool.o \ + cram/vlen.o \ + cram/zfio.o + +PLUGIN_OBJS = + +cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) +cram_io_h = cram/cram_io.h $(cram_misc_h) +cram_misc_h = cram/misc.h cram/os.h +cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) +cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) +cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) +cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h +hfile_internal_h = hfile_internal.h $(htslib_hfile_h) +hts_internal_h = hts_internal.h $(htslib_hts_h) + + +# To be effective, config.mk needs to appear after most Makefile variables are +# set but before most rules appear, so that it can both use previously-set +# variables in its own rules' prerequisites and also update variables for use +# in later rules' prerequisites. + +# If your make doesn't accept -include, change this to 'include' if you are +# using the configure script or just comment the line out if you are not. +-include config.mk + +# Usually config.h is generated by running configure or config.status, +# but if those aren't used create a default config.h here. +config.h: + echo '/* Empty config.h generated by Makefile */' > $@ + + +lib-static: libhts.a + +# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have +# GNU Make, comment out the parts of this conditional that don't apply. +PLATFORM := $(shell uname -s) +ifeq "$(PLATFORM)" "Darwin" +SHLIB_FLAVOUR = dylib +lib-shared: libhts.dylib +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) +else +SHLIB_FLAVOUR = so +lib-shared: libhts.so +BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) +endif + +plugins: $(BUILT_PLUGINS) + + +libhts.a: $(LIBHTS_OBJS) + @-rm -f $@ + $(AR) -rc $@ $(LIBHTS_OBJS) + -$(RANLIB) $@ + + +# The target here is libhts.so, as that is the built file that other rules +# depend upon and that is used when -lhts appears in other program's recipes. +# As a byproduct invisible to make, libhts.so.NN is also created, as it is the +# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + +libhts.so: $(LIBHTS_OBJS:.o=.pico) + $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + +# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH +# includes this project's build directory). + +libhts.dylib: $(LIBHTS_OBJS) + $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + +.pico.so: + $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) + +.o.bundle: + $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) + + +bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) +kstring.o kstring.pico: kstring.c $(htslib_kstring_h) +knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) +hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) +hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) +hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) +hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) +vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) +sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) +tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) +faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) +synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) +vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) +vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) +kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) +regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) +md5.o md5.pico: md5.c config.h $(htslib_hts_h) +plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) + +cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) +cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) +cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) +cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) +cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) +cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) +cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h +cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) +cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h +cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) +cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h +cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h +cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h +cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h +cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h +cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h +cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h + + +bgzip: bgzip.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) + +htsfile: htsfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) + +tabix: tabix.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) + +bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) +htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) +tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) + + +# For tests that might use it, set $REF_PATH explicitly to use only reference +# areas within the test suite (or set it to ':' to use no reference areas). +check test: htsfile $(BUILT_TEST_PROGRAMS) + test/fieldarith test/fieldarith.sam + test/hfile + test/sam test/ce.fa test/faidx.fa + test/test-regidx + cd test && REF_PATH=: ./test_view.pl + cd test && REF_PATH=: ./test.pl + +test/fieldarith: test/fieldarith.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) + +test/hfile: test/hfile.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) + +test/sam: test/sam.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) + +test/test-regidx: test/test-regidx.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) + +test/test_view: test/test_view.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) + +test/test-vcf-api: test/test-vcf-api.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) + +test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a + $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) + +test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) +test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) +test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) +test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) +test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) +test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) +test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) + + +install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig + $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) + if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi + $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib + $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a + $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) + $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) + +installdirs: + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) + if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi + +# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, +# with symlinks libhts.so (used via -lhts during linking of client programs) +# and libhts.so.NN (used by client executables at runtime). + +install-so: libhts.so installdirs + $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so + ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) + +install-dylib: libhts.dylib installdirs + $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib + ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib + +# Substitute these pseudo-autoconf variables only at install time +# so that "make install prefix=/prefix/path" etc continue to work. +install-pkgconfig: installdirs + sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc + chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc + +# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides +# flags for building against the uninstalled library in this build directory. +htslib-uninstalled.pc: htslib.pc.in + sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ + + +testclean: + -rm -f test/*.tmp test/*.tmp.* + +mostlyclean: testclean + -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h + +clean: mostlyclean clean-$(SHLIB_FLAVOUR) + -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) + +distclean maintainer-clean: clean + -rm -f config.cache config.h config.log config.mk config.status + -rm -f TAGS *-uninstalled.pc + +clean-so: + -rm -f libhts.so libhts.so.* + +clean-dylib: + -rm -f libhts.dylib libhts.*.dylib + + +tags TAGS: + ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h + +# We recommend libhts-using programs be built against a separate htslib +# installation. However if you feel that you must bundle htslib source +# code with your program, this hook enables Automake-style "make dist" +# for this subdirectory. If you do bundle an htslib snapshot, please +# add identifying information to $(PACKAGE_VERSION) as appropriate. +# (The wildcards attempt to omit non-exported files (.git*, README.md, +# etc) and other detritus that might be in the top-level directory.) +distdir: + tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) + +cd $(distdir) && $(MAKE) distclean + +force: + + +.PHONY: all check clean distclean distdir force +.PHONY: install install-pkgconfig installdirs lib-shared lib-static +.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean +.PHONY: clean-so install-so +.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/diff b/easybuild/easyconfigs/r/RSEM/sam/hts/diff new file mode 100644 index 0000000000..97af9b3e44 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/sam/hts/diff @@ -0,0 +1,18 @@ +--- Makefile.orig 2016-05-13 12:08:45.000000000 +0200 ++++ Makefile 2016-05-13 12:10:21.000000000 +0200 +@@ -22,13 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + AR = ar + RANLIB = ranlib + + CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic + LDFLAGS = + LIBS = -- GitLab From 703061c2172a007d4150587ff2caaa4d4d315237 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:11:34 +0200 Subject: [PATCH 0841/2403] add easyconfig tvb-data-20160209-intel-2016a-Python-2.7.11.eb, add easyconfig tvb-framework-20160329-intel-2016a-Python-2.7.11.eb, add easyconfig tvb-library-20160416-intel-2016a-Python-2.7.11.eb, add easyconfig psutil-4.1.0-intel-2016a-Python-2.7.11.eb --- .../psutil-4.1.0-intel-2016a-Python-2.7.11.eb | 25 +++++++++++ ...data-20160209-intel-2016a-Python-2.7.11.eb | 40 +++++++++++++++++ ...work-20160329-intel-2016a-Python-2.7.11.eb | 43 +++++++++++++++++++ ...rary-20160416-intel-2016a-Python-2.7.11.eb | 40 +++++++++++++++++ 4 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..add4ca70ed --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-4.1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/psutil' +description = """psutil is a cross-platform library for retrieving information onrunning processes and + system utilization (CPU, memory, disks, network)in Python.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..313af45870 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-data/tvb-data-20160209-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'tvb-data' +version = '20160209' +commit = '8f46bd7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + Various demonstration data for use with TVB.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-data/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb_data'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1a013dadc1 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'tvb-framework' +version = '20160329' +commit = '7e6c51a977136a7ca44988f24914bff700168013' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-framework/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['tvb-framework-%(version)s_no-fixed-matplotlib.patch'] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), + ('psutil', '4.1.0', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.core'} + +sanity_check_paths = { + 'files': ['tvb-framework-%s/tvb/config/logger/logger_config.conf' % commit], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f3c72162a8 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-library/tvb-library-20160416-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'tvb-library' +version = '20160416' +commit = '20172bc' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-library/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), # provides numpy, Cython + ('networkx', '1.11', versionsuffix), + ('numexpr', '2.5.2', versionsuffix), + ('gdist', '1.0.3', versionsuffix), + ('NiBabel', '2.0.2', versionsuffix), + ('scikit-learn', '0.17.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('lxml', '3.5.0', versionsuffix), + ('h5py', '2.5.0', versionsuffix + '-HDF5-1.8.16'), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.simulator'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 509a51519bd4e1bcd63fdca1a7e20aff7606391e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:13:02 +0200 Subject: [PATCH 0842/2403] add patch file for tvb-framework --- ...vb-framework-20160329_no-fixed-matplotlib.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch new file mode 100644 index 0000000000..8983c5f8ea --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20160329_no-fixed-matplotlib.patch @@ -0,0 +1,14 @@ +--- setup.py.orig 2016-03-29 08:34:20.000000000 +0200 ++++ setup.py 2016-04-28 15:27:35.764121169 +0200 +@@ -47,9 +47,9 @@ + TVB_TEAM += "Stuart Knock, Marmaduke Woodman, Paula Sansz Leon, " + + TVB_INSTALL_REQUIREMENTS = ["apscheduler", "beautifulsoup", "cherrypy", "genshi", "cfflib", "formencode==1.3.0a1", +- "h5py==2.3.0", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", ++ "h5py", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", + "numexpr", "psutil", "scikit-learn", "scipy", "simplejson", "Pillow", +- "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib==1.2.1"] ++ "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib"] + + EXCLUDE_INTROSPECT_FOLDERS = [folder for folder in os.listdir(".") + if os.path.isdir(os.path.join(".", folder)) and folder != "tvb"] -- GitLab From e628bb6ac7329c3cca02d1b31e3e1799fedf8a20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 14:22:50 +0200 Subject: [PATCH 0843/2403] add easyconfig networkx-1.11-intel-2016a-Python-2.7.11.eb --- ...networkx-1.11-intel-2016a-Python-2.7.11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..43100d8ffb --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'tools' -- GitLab From a5f6b02a3abef0ce392d411fb4ad70a220b74bac Mon Sep 17 00:00:00 2001 From: Javier Ruiz Date: Fri, 13 May 2016 09:36:24 -0400 Subject: [PATCH 0844/2403] use %(pyshortver)s rather than hardcoding 2.7 --- .../m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb index 6bb8c242f7..cc883fdc72 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-foss-2016a-Python-2.7.11.eb @@ -19,7 +19,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/python2.7/site-packages/minieigen.%s' % SHLIB_EXT], + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb index e96c03e7a3..139241b97c 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016a-Python-2.7.11.eb @@ -32,7 +32,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -preinstallopts = "mkdir -p %(installdir)s/lib/python2.7/site-packages/ && " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From 74c659030a52fb2edba7a07203ece1637ad96c42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 17:15:57 +0200 Subject: [PATCH 0845/2403] add easyconfig TVB-20160416-intel-2016a-Python-2.7.11.eb --- .../TVB-20160416-intel-2016a-Python-2.7.11.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..5a7b80d98f --- /dev/null +++ b/easybuild/easyconfigs/t/TVB/TVB-20160416-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,20 @@ +easyblock = 'Bundle' + +name = 'TVB' +version = '20160416' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://thevirtualbrain.org' +description = """The Virtual Brain will deliver the first open simulation of the human brain + based on individual large-scale connectivity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('tvb-data', '20160209', versionsuffix), + ('tvb-framework', '20160329', versionsuffix), + ('tvb-library', version, versionsuffix), +] +hiddendependencies = dependencies[:] + +moduleclass = 'bio' -- GitLab From b5e99de36919a3cef7f6ecaf4eb437dc0c9ea0c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 19:29:55 +0200 Subject: [PATCH 0846/2403] include numactl as an explicit dependency in hwloc easyconfigs using PGI toolchain --- .../h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 5 ++++- .../h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb index 54ea46766a..7ea9401fcd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] -# numactl is a direct dependency of PGI +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '4.9.3')), +] + configopts = "--enable-libnuma=$EBROOTNUMACTL" moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb index 1b876ae44f..e7bd276c18 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] -# numactl is a direct dependency of PGI +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.3.0')), +] + configopts = "--enable-libnuma=$EBROOTNUMACTL" moduleclass = 'system' -- GitLab From 37195fcce4756ed239ace629e7e566e896098825 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 May 2016 19:41:33 +0200 Subject: [PATCH 0847/2403] break up long lines --- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb | 3 ++- easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb index 18ef21e40a..02a330d8d9 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-foss-2016a.eb @@ -2,7 +2,8 @@ name = 'SuperLU' version = '5.1.1' homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb index 411ef70cfb..533110bf6f 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-ictce-7.3.5.eb @@ -2,7 +2,8 @@ name = 'SuperLU' version = '5.1.1' homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' -description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} toolchainopts = {'opt': True, 'pic': True} -- GitLab From a875c3f2016b1847c5f948bbc31826e582b655d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 10:05:16 +0200 Subject: [PATCH 0848/2403] correct install location of OpenCV Python bindings --- .../o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 18 ++++++------------ .../o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 18 ++++++------------ 3 files changed, 14 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 89e2746bd8..00815da8bc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -39,7 +39,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -56,7 +56,7 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 96d8323ca5..4231bf81f8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -23,22 +23,16 @@ builddependencies = [ ('CMake', '3.0.0'), ] -python = 'Python' -pythonver = '2.7.8' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -java = 'Java' -javaver = '1.7.0_79' - dependencies = [ - (python, pythonver), + ('Python', '2.7.8'), ('zlib', '1.2.8'), ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver, '', True), - ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), + ('Java', '1.7.0_79', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] @@ -46,7 +40,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -63,13 +57,13 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } modextrapaths = { - 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'CLASSPATH': 'share/OpenCV/java', } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index 776b0d7db5..bf5ac8dc56 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -23,22 +23,16 @@ builddependencies = [ ('CMake', '3.0.0'), ] -python = 'Python' -pythonver = '2.7.8' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -java = 'Java' -javaver = '1.7.0_60' - dependencies = [ - (python, pythonver), + ('Python', '2.7.8'), ('zlib', '1.2.8'), ('FFmpeg', '2.4'), ('libjpeg-turbo', '1.3.1'), ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - (java, javaver, '', True), - ('ant', '1.9.3', '-%s-%s' % (java, javaver), True), + ('Java', '1.7.0_60', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] @@ -46,7 +40,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' -configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' @@ -63,13 +57,13 @@ configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/cv2.so'] + ['bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade']], 'dirs': ['include'] } modextrapaths = { - 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'CLASSPATH': 'share/OpenCV/java', } -- GitLab From f4cb5ad5f931bd3aa471efece5a65b73093ec3be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 12:24:22 +0200 Subject: [PATCH 0849/2403] add comment + author in patch for Score-P 2.0.1 --- .../s/Score-P/Score-P-2.0.1_fix_score_configure.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch index c387be0132..53c43dee48 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1_fix_score_configure.patch @@ -1,3 +1,5 @@ +prevent build-score/configure from picking up $CFLAGS etc., backported from Score-P 2.0.2 +author: Markus Geimer (JSC) --- build-score/configure.orig 2016-05-11 09:21:03.716441529 +0200 +++ build-score/configure 2016-05-11 09:38:14.651525955 +0200 @@ -735,6 +735,7 @@ afs_srcdir -- GitLab From 666589950123850517c4a0ef406a349fe131aca7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 12:26:11 +0200 Subject: [PATCH 0850/2403] include XZ as dependency for libunwind --- .../easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 9583401685..ac65492ae4 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -19,6 +19,12 @@ checksums = [ 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz ] +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] -- GitLab From 3c768a72fc16a6857a8610314ba3dd430e54280f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 14:38:44 +0200 Subject: [PATCH 0851/2403] include XZ as dependency for libunwind --- .../l/libunwind/libunwind-1.1-foss-2015a.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 10 ++++++++++ 3 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 74be1e3d78..15053fb3db 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,6 +15,16 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 957e854ad9..6d87f10400 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,6 +15,16 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 5059851443..6e07f18865 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'dirs': [] -- GitLab From bcd1bb2e559a20366e4a21b88288c527c0be982b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 14:47:15 +0200 Subject: [PATCH 0852/2403] add easyconfigs for XZ dependencies --- .../a/Automake/Automake-1.15-ictce-5.3.0.eb | 33 +++++++++++++++++++ .../Autotools-20150215-ictce-5.3.0.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-ictce-5.3.0.eb | 17 ++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb | 30 +++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 30 +++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 30 +++++++++++++++++ 6 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..cc76e86a61 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb new file mode 100644 index 0000000000..36c5a28f14 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb new file mode 100644 index 0000000000..1b3599b1ed --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.16')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb new file mode 100644 index 0000000000..049e77b657 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.4'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..f9a06be732 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215', '', ('GCC', '4.7.2')), +] + +dependencies = [ + ('gettext', '0.18.2'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..96fe0ea8c8 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.18.2'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 725123396f9aa06459af3c612f72f54387af45e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:38:26 +0200 Subject: [PATCH 0853/2403] define with_shared_libs by comparing OS_TYPE with 'Linux' --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 460cd7abe7..46b2debed4 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.bzip.org/%(version)s/'] buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" -# disable building of shared libraries, doesn't work everywhere (e.g. on OS X, where 'gcc' is actually Clang...) -with_shared_libs = False +# building of shared libraries doesn't work on OS X (where 'gcc' is actually Clang...) +with_shared_libs = OS_TYPE == 'Linux' moduleclass = 'tools' -- GitLab From 3abec3c98df891559a3bc73262ab41a7a9464cd7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:47:25 +0200 Subject: [PATCH 0854/2403] remove duplicate non-version patch for DIAL --- easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch b/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch deleted file mode 100644 index d5a95a417e..0000000000 --- a/easybuild/easyconfigs/d/DIAL/DIAL-Makefile.in.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- DIAL/src/Makefile.in 2015-02-10 14:10:33.143293723 +0100 -+++ DIAL/src/Makefile.in 2015-02-10 14:10:39.462384572 +0100 -@@ -246,7 +246,7 @@ - @DEBUG_FALSE@@PROFILE_FALSE@@TESTING_TRUE@OPTIMIZATIONS = -ggdb - @DEBUG_FALSE@@PROFILE_TRUE@OPTIMIZATIONS = -ggdb -pg -DNDEBUG -O2 -funroll-all-loops $(ARCH) - @DEBUG_TRUE@OPTIMIZATIONS = -ggdb -DDEBUG --AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror \ -+AM_CFLAGS = -W -Wformat -Wimplicit -Wreturn-type -Wall \ - -Wunused-variable -Wunused-parameter -Wreturn-type -Wswitch \ - -Wcast-align -Winline -Wnested-externs -Wextra $(OPTIMIZATIONS) \ - -std=c99 -- GitLab From 218e9baa654a501e04a87d6b2d9172183cae1435 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 May 2016 15:48:23 +0200 Subject: [PATCH 0855/2403] fix typo in DIAL easyconfig --- easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 9f8127a929..0edd0228ed 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -26,7 +26,7 @@ binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'c 'update_status',] sanity_check_paths = { - 'files': ['bin/%s' % bin for binfile in binaries], + 'files': ['bin/%s' % binfile for binfile in binaries], 'dirs': ['bin'] } -- GitLab From 65f54a4918f04358a8bdd4499180b8def5499dbb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 14 May 2016 21:28:22 +0100 Subject: [PATCH 0856/2403] Add comment explaining use of upstream unconventional versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index af32067597..110e6af4ca 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -5,6 +5,7 @@ easyblock = 'Tarball' name = 'annovar' +# Unconventional version is taken from the upstream site version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From 4c77a1e79fcbea5cca7ead451a94d31e12c5b832 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 14 May 2016 21:32:45 +0100 Subject: [PATCH 0857/2403] Add comment explaining use of upstream unconventional versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index eacaffe6ed..14f3ea6b69 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -5,6 +5,7 @@ easyblock = 'Tarball' name = 'annovar' +# UNconventional versioning is taken from upstream version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From e8b33b6a01ce3b1d8cf8020162a6fe08250e0346 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 May 2016 11:48:39 +0200 Subject: [PATCH 0858/2403] add patch to fix broken OpenSSL tests due to expired certificates --- .../o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb | 2 + .../OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb | 2 + .../OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb | 2 + .../OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb | 2 + .../OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb | 5 +- .../OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb | 5 +- .../OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb | 8 +- .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb | 5 + .../o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb | 2 +- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 1 + .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb | 5 +- .../OpenSSL-1.0.x_fix-tests-certs.patch | 579 ++++++++++++++++++ 37 files changed, 669 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb index 11891cf96a..31798451a4 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb index b20db23b0a..d8b87dfdff 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goalf-1.1.0-no-OFED.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb index db9d43d1ce..fbc79c380f 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-goolf-1.4.10.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb index 413c8374f6..4654b89426 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-GCC-4.8.2.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb index ad1d42662f..b65d36ca86 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmpolf-1.1.6.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb index 533a7cef1c..bbd1b1d7f0 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.1.12rc1.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb index 0a8200f83c..df0e78c6e2 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgmvolf-1.2.7.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb index 973932317d..1da82cfc0b 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-cgoolf-1.1.7.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb index 707bd90aa3..35f8ec876d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb index 9b0c99840e..18a5bc06b4 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-gmvolf-1.7.12rc1.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb index 1f693bfc6b..090668fbfb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb index 0b7691ae3d..edb92686ac 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb index 4edbca03d8..ef533a11f5 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] +patches = [ + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb index 908a928059..1609277d54 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-3.2.2.u3.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb index 7029f97900..62338512e9 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb @@ -12,9 +12,11 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1f-fix_pod_syntax-1.patch'] - -patches = ['OpenSSL-1.0.1f_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb index 4c9a5a74b5..bf52ea9bcc 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb index a9093ec8b3..a0eb2be098 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb index 4050211bd7..055777f95e 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.4.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb index 14f3a0762b..b401f764ea 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1f-fix_pod_syntax-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb index 5cfad5f0b3..ca90aecbb3 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-iqacml-3.7.3.eb @@ -12,6 +12,11 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] + dependencies = [('zlib', '1.2.7')] configopts = "shared no-ssl2 no-ssl3" diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb index d31ac88a20..aec4b94ad1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1i-intel-2014b.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb index 39a21a3a41..e10bf5f0ac 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-GCC-4.9.2.eb @@ -14,6 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb index 7815b2d7b3..20662edace 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.14.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb index 895b5bd87b..668e579ba1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-goolf-1.5.16.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb index 3ffb667048..91cb41c8eb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index a127a7e7bb..307f185342 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -15,6 +15,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index 6800732437..c4f94fabf9 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb index a6496a921f..108fade18d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb index 733ddd9ac4..8c74a57361 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb index 9e06d07cee..4d4f0712ca 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb index a34f9121d1..654b06cdb8 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb index 17db49d12f..470877ecda 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb index 3a69395fe3..1c6c615bff 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1q-intel-2015b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb index 9c3838a1b7..df437ed5a6 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1r-foss-2015b.eb @@ -12,6 +12,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] + dependencies = [('zlib', '1.2.8')] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb index a5aab91ad9..5cf77af391 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-foss-2016a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1q_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb index 976aa24ab2..517a86ba16 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1s-intel-2016a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-1.0.1q_icc-fixes.patch'] +patches = [ + 'OpenSSL-1.0.1q_icc-fixes.patch', + 'OpenSSL-1.0.x_fix-tests-certs.patch', +] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch new file mode 100644 index 0000000000..9bc7df2d14 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.x_fix-tests-certs.patch @@ -0,0 +1,579 @@ +fix broken tests by updating S/MIME certificates +https://github.com/openssl/openssl/commit/24762dee178bace3c3 +diff --git a/test/smime-certs/smdsa1.pem b/test/smime-certs/smdsa1.pem +index d5677db..b424f67 100644 +--- a/test/smime-certs/smdsa1.pem ++++ b/test/smime-certs/smdsa1.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBuwIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGATQlPPF+OeU8nu3rsdXGDiZdJzOkuCce3KQfTABA9C+Dk4CVcvBdd +-YRLGpnykumkNTO1sTO+4/Gphsuje1ujK9td4UEhdYqylCe5QjEMrszDlJtelDQF9 +-C0yhdjKGTP0kxofLhsGckcuQvcKEKffT2pDDKJIy4vWQO0UyJl1vjLcCFG2uiGGx +-9fMUZq1v0ePD4Wo0Xkxo +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZQIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQjAiEAkolGvb/76X3vm5Ov09ezqyBYt9cdj/FLH7DyMkxO7X0= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpDCCAw2gAwIBAgIJAMtotfHYdEsWMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBDMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzEwggG3MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhAACgYBN +-CU88X455Tye7eux1cYOJl0nM6S4Jx7cpB9MAED0L4OTgJVy8F11hEsamfKS6aQ1M +-7WxM77j8amGy6N7W6Mr213hQSF1irKUJ7lCMQyuzMOUm16UNAX0LTKF2MoZM/STG +-h8uGwZyRy5C9woQp99PakMMokjLi9ZA7RTImXW+Mt6OBgzCBgDAdBgNVHQ4EFgQU +-4Qfbhpi5yqXaXuCLXj427mR25MkwHwYDVR0jBBgwFoAUE89Lp7uJLrM4Vxd2xput +-aFvl7RcwDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBsAwIAYDVR0RBBkwF4EV +-c21pbWVkc2ExQG9wZW5zc2wub3JnMA0GCSqGSIb3DQEBBQUAA4GBAFrdUzKK1pWO +-kd02S423KUBc4GWWyiGlVoEO7WxVhHLJ8sm67X7OtJOwe0UGt+Nc5qLtyJYSirw8 +-phjiTdNpQCTJ8+Kc56tWkJ6H7NAI4vTJtPL5BM/EmeYrVSU9JI9xhqpyKw9IBD+n +-hRJ79W9FaiJRvaAOX+TkyTukJrxAWRyv ++ZXN0IFMvTUlNRSBFRSBEU0EgIzEwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAGXSQADbuRIZBjiQ6NikwZl+x ++EDEffIE0RWbvwf1tfWxw4ZvanO/djyz5FePO0AIJDBCLUjr9D32nkmIG1Hu3dWgV ++86knQsM6uFiMSzY9nkJGZOlH3w4NHLE78pk75xR1sg1MEZr4x/t+a/ea9Y4AXklE ++DCcaHtpMGeAx3ZAqSKec+zQOOA73JWP1/gYHGdYyTQpQtwRTsh0Gi5mOOdpoJ0vp ++O83xYbFCZ+ZZKX1RWOjJe2OQBRtw739q1nRga1VMLAT/LFSQsSE3IOp8hiWbjnit ++1SE6q3II2a/aHZH/x4OzszfmtQfmerty3eQSq3bgajfxCsccnRjSbLeNiazRSKNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFNHQYTOO ++xaZ/N68OpxqjHKuatw6sMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQAAiLociMMXcLkO/uKjAjCIQMrsghrOrxn4ZGBx ++d/mCTeqPxhcrX2UorwxVCKI2+Dmz5dTC2xKprtvkiIadJamJmxYYzeF1pgRriFN3 ++MkmMMkTbe/ekSvSeMtHQ2nHDCAJIaA/k9akWfA0+26Ec25/JKMrl3LttllsJMK1z ++Xj7TcQpAIWORKWSNxY/ezM34+9ABHDZB2waubFqS+irlZsn38aZRuUI0K67fuuIt ++17vMUBqQpe2hfNAjpZ8dIpEdAGjQ6izV2uwP1lXbiaK9U4dvUqmwyCIPniX7Hpaf ++0VnX0mEViXMT6vWZTjLBUv0oKmO7xBkWHIaaX6oyF32pK5AO + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smdsa2.pem b/test/smime-certs/smdsa2.pem +index ef86c11..648447f 100644 +--- a/test/smime-certs/smdsa2.pem ++++ b/test/smime-certs/smdsa2.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBvAIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGBAIPmO8BtJ+Yac58trrPwq9b/6VW3jQTWzTLWSH84/QQdqQa+Pz3v +-It/+hHM0daNF5uls8ICsPL1aLXmRx0pHvIyb0aAzYae4T4Jv/COPDMTdKbA1uitJ +-VbkGZrm+LIrs7I9lOkb4T0vI6kL/XdOCXY1469zsqCgJ/O2ibn6mq0nWAhR716o2 +-Nf8SimTZYB0/CKje6M5ufA== +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZAIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQiAiAdCUJ5n2Q9hIynN8BMpnRcdfH696BKejGx+2Mr2kfnnA== ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpTCCAw6gAwIBAgIJAMtotfHYdEsXMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBEMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzIwggG4MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhQACgYEA +-g+Y7wG0n5hpzny2us/Cr1v/pVbeNBNbNMtZIfzj9BB2pBr4/Pe8i3/6EczR1o0Xm +-6WzwgKw8vVoteZHHSke8jJvRoDNhp7hPgm/8I48MxN0psDW6K0lVuQZmub4siuzs +-j2U6RvhPS8jqQv9d04JdjXjr3OyoKAn87aJufqarSdajgYMwgYAwHQYDVR0OBBYE +-FHsAGNfVltSYUq4hC+YVYwsYtA+dMB8GA1UdIwQYMBaAFBPPS6e7iS6zOFcXdsab +-rWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgbAMCAGA1UdEQQZMBeB +-FXNtaW1lZHNhMkBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQCx9BtCbaYF +-FXjLClkuKXbESaDZA1biPgY25i00FsUzARuhCpqD2v+0tu5c33ZzIhL6xlvBRU5l +-6Atw/xpZhae+hdBEtxPJoGekLLrHOau7Md3XwDjV4lFgcEJkWZoaSOOIK+4D5jF0 +-jZWtHjnwEzuLYlo7ScHSsbcQfjH0M1TP5A== ++ZXN0IFMvTUlNRSBFRSBEU0EgIzIwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAItQlFu0t7Mw1HHROuuwKLS+E ++h2WNNZP96MLQTygOVlqgaJY+1mJLzvl/51LLH6YezX0t89Z2Dm/3SOJEdNrdbIEt ++tbu5rzymXxFhc8uaIYZFhST38oQwJOjM8wFitAQESe6/9HZjkexMqSqx/r5aEKTa ++LBinqA1BJRI72So1/1dv8P99FavPADdj8V7fAccReKEQKnfnwA7mrnD+OlIqFKFn ++3wCGk8Sw7tSJ9g6jgCI+zFwrKn2w+w+iot/Ogxl9yMAtKmAd689IAZr5GPPvV2y0 ++KOogCiUYgSTSawZhr+rjyFavfI5dBWzMq4tKx/zAi6MJ+6hGJjJ8jHoT9JAPmaNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFGaxw04k ++qpufeGZC+TTBq8oMnXyrMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQCk2Xob1ICsdHYx/YsBzY6E1eEwcI4RZbZ3hEXp ++VA72/Mbz60gjv1OwE5Ay4j+xG7IpTio6y2A9ZNepGpzidYcsL/Lx9Sv1LlN0Ukzb ++uk6Czd2sZJp+PFMTTrgCd5rXKnZs/0D84Vci611vGMA1hnUnbAnBBmgLXe9pDNRV ++6mhmCLLjJ4GOr5Wxt/hhknr7V2e1VMx3Q47GZhc0o/gExfhxXA8+gicM0nEYNakD ++2A1F0qDhQGakjuofANHhjdUDqKJ1sxurAy80fqb0ddzJt2el89iXKN+aXx/zEX96 ++GI5ON7z/bkVwIi549lUOpWb2Mved61NBzCLKVP7HSuEIsC/I + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smdsa3.pem b/test/smime-certs/smdsa3.pem +index eeb848d..77acc5e 100644 +--- a/test/smime-certs/smdsa3.pem ++++ b/test/smime-certs/smdsa3.pem +@@ -1,34 +1,47 @@ +------BEGIN DSA PRIVATE KEY----- +-MIIBvAIBAAKBgQDFJfsIPOIawMO5biw+AoYUhNVxReBOLQosU3Qv4B8krac0BNr3 +-OjSGLh1wZxHqhlAE0QmasTaKojuk20nNWeFnczSz6vDl0IVJEhS8VYor5kt9gLqt +-GcoAgsf4gRDIutJyQDaNn3IVY89uXUVIoexvQeLQDBCgQPC5O8rJdqBwtwIVAK2J +-jt+dqk07eQUE59koYUEKyNorAoGBAI4IEpusf8G14kCHmRtnHXM2tG5EWJDmW6Qt +-wjqvWp1GKUx5WFy1tVWR9nl5rL0Di+kNdENo+SkKj7h3uDulGOI6T0mQYbV2h1IK +-+FMOGnOqvZ8eNTE2n4PGTo5puZ63LBm+QYrQsrNiUY4vakLFQ2rEK/SLwdsDFK4Z +-SJCBQw5zAoGAYzOpPmh8Je1IDauEXhgaLz14wqYUHHcrj2VWVJ6fRm8GhdQFJSI7 +-GUk08pgKZSKic2lNqxuzW7/vFxKQ/nvzfytY16b+2i+BR4Q6yvMzCebE1hHVg0Ju +-TwfUMwoFEOhYP6ZwHSUiQl9IBMH9TNJCMwYMxfY+VOrURFsjGTRUgpwCFQCIGt5g +-Y+XZd0Sv69CatDIRYWvaIA== +------END DSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIICZQIBADCCAjkGByqGSM44BAEwggIsAoIBAQCQfLlNdehPnTrGIMhw4rk0uua6 ++k1nCG3zcyfXli17BdB2k0HBPaTA3a3ZHfOt1Awy0Uu0wZ3gdPr9z0I64hnJXIGou ++zIanZ7nYRImHtX5JMFbXeyxo1Owd2Zs3oEk9nQUoUsMxvmYC/ghPL5Zx1pPxcHCO ++wzWxoG4yZMjimXOc1/W7zvK/4/g/Cz9fItD3zdcydfgM/hK0/CeYQ21xfhqf4mjK ++v9plnCcWgToGI+7H8VK80MFbkO2QKRz3vP1/TjK6PRm9sEeB5b10+SvGv2j2w+CC ++0fXL4s6n7PtBlm/bww8xL1/Az8kwejUcII1Dc8uNwwISwGbwaGBvl7IHpm21AiEA ++rodZi+nCKZdTL8IgCjX3n0DuhPRkVQPjz/B6VweLW9MCggEAfimkUNwnsGFp7mKM ++zJKhHoQkMB1qJzyIHjDzQ/J1xjfoF6i27afw1/WKboND5eseZhlhA2TO5ZJB6nGx ++DOE9lVQxYVml++cQj6foHh1TVJAgGl4mWuveW/Rz+NEhpK4zVeEsfMrbkBypPByy ++xzF1Z49t568xdIo+e8jLI8FjEdXOIUg4ehB3NY6SL8r4oJ49j/sJWfHcDoWH/LK9 ++ZaBF8NpflJe3F40S8RDvM8j2HC+y2Q4QyKk1DXGiH+7yQLGWzr3M73kC3UBnnH0h ++Hxb7ISDCT7dCw/lH1nCbVFBOM0ASI26SSsFSXQrvD2kryRcTZ0KkyyhhoPODWpU+ ++TQMsxQQjAiEArJr6p2zTbhRppQurHGTdmdYHqrDdZH4MCsD9tQCw1xY= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIIDpDCCAw2gAwIBAgIJAMtotfHYdEsYMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIFkDCCBHigAwIBAgIJANk5lu6mSyBFMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzFaFw0yMzA1MjYxNzI4MzFaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBEU0EgIzMwggG3MIIBLAYHKoZIzjgEATCCAR8CgYEAxSX7 +-CDziGsDDuW4sPgKGFITVcUXgTi0KLFN0L+AfJK2nNATa9zo0hi4dcGcR6oZQBNEJ +-mrE2iqI7pNtJzVnhZ3M0s+rw5dCFSRIUvFWKK+ZLfYC6rRnKAILH+IEQyLrSckA2 +-jZ9yFWPPbl1FSKHsb0Hi0AwQoEDwuTvKyXagcLcCFQCtiY7fnapNO3kFBOfZKGFB +-CsjaKwKBgQCOCBKbrH/BteJAh5kbZx1zNrRuRFiQ5lukLcI6r1qdRilMeVhctbVV +-kfZ5eay9A4vpDXRDaPkpCo+4d7g7pRjiOk9JkGG1dodSCvhTDhpzqr2fHjUxNp+D +-xk6OabmetywZvkGK0LKzYlGOL2pCxUNqxCv0i8HbAxSuGUiQgUMOcwOBhAACgYBj +-M6k+aHwl7UgNq4ReGBovPXjCphQcdyuPZVZUnp9GbwaF1AUlIjsZSTTymAplIqJz +-aU2rG7Nbv+8XEpD+e/N/K1jXpv7aL4FHhDrK8zMJ5sTWEdWDQm5PB9QzCgUQ6Fg/ +-pnAdJSJCX0gEwf1M0kIzBgzF9j5U6tREWyMZNFSCnKOBgzCBgDAdBgNVHQ4EFgQU +-VhpVXqQ/EzUMdxLvP7o9EhJ8h70wHwYDVR0jBBgwFoAUE89Lp7uJLrM4Vxd2xput +-aFvl7RcwDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBsAwIAYDVR0RBBkwF4EV +-c21pbWVkc2EzQG9wZW5zc2wub3JnMA0GCSqGSIb3DQEBBQUAA4GBACM9e75EQa8m +-k/AZkH/tROqf3yeqijULl9x8FjFatqoY+29OM6oMGM425IqSkKd2ipz7OxO0SShu +-rE0O3edS7DvYBwvhWPviRaYBMyZ4iFJVup+fOzoYK/j/bASxS3BHQBwb2r4rhe25 +-OlTyyFEk7DJyW18YFOG97S1P52oQ5f5x ++ZXN0IFMvTUlNRSBFRSBEU0EgIzMwggNGMIICOQYHKoZIzjgEATCCAiwCggEBAJB8 ++uU116E+dOsYgyHDiuTS65rqTWcIbfNzJ9eWLXsF0HaTQcE9pMDdrdkd863UDDLRS ++7TBneB0+v3PQjriGclcgai7MhqdnudhEiYe1fkkwVtd7LGjU7B3ZmzegST2dBShS ++wzG+ZgL+CE8vlnHWk/FwcI7DNbGgbjJkyOKZc5zX9bvO8r/j+D8LP18i0PfN1zJ1 +++Az+ErT8J5hDbXF+Gp/iaMq/2mWcJxaBOgYj7sfxUrzQwVuQ7ZApHPe8/X9OMro9 ++Gb2wR4HlvXT5K8a/aPbD4ILR9cvizqfs+0GWb9vDDzEvX8DPyTB6NRwgjUNzy43D ++AhLAZvBoYG+XsgembbUCIQCuh1mL6cIpl1MvwiAKNfefQO6E9GRVA+PP8HpXB4tb ++0wKCAQB+KaRQ3CewYWnuYozMkqEehCQwHWonPIgeMPND8nXGN+gXqLbtp/DX9Ypu ++g0Pl6x5mGWEDZM7lkkHqcbEM4T2VVDFhWaX75xCPp+geHVNUkCAaXiZa695b9HP4 ++0SGkrjNV4Sx8ytuQHKk8HLLHMXVnj23nrzF0ij57yMsjwWMR1c4hSDh6EHc1jpIv ++yvignj2P+wlZ8dwOhYf8sr1loEXw2l+Ul7cXjRLxEO8zyPYcL7LZDhDIqTUNcaIf ++7vJAsZbOvczveQLdQGecfSEfFvshIMJPt0LD+UfWcJtUUE4zQBIjbpJKwVJdCu8P ++aSvJFxNnQqTLKGGg84NalT5NAyzFA4IBBQACggEAcXvtfiJfIZ0wgGpN72ZeGrJ9 ++msUXOxow7w3fDbP8r8nfVkBNbfha8rx0eY6fURFVZzIOd8EHGKypcH1gS6eZNucf ++zgsH1g5r5cRahMZmgGXBEBsWrh2IaDG7VSKt+9ghz27EKgjAQCzyHQL5FCJgR2p7 ++cv0V4SRqgiAGYlJ191k2WtLOsVd8kX//jj1l8TUgE7TqpuSEpaSyQ4nzJROpZWZp ++N1RwFmCURReykABU/Nzin/+rZnvZrp8WoXSXEqxeB4mShRSaH57xFnJCpRwKJ4qS ++2uhATzJaKH7vu63k3DjftbSBVh+32YXwtHc+BGjs8S2aDtCW3FtDA7Z6J8BIxaNg ++MF4wDAYDVR0TAQH/BAIwADAOBgNVHQ8BAf8EBAMCBeAwHQYDVR0OBBYEFMJxatDE ++FCEFGl4uoiQQ1050Ju9RMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZs ++MA0GCSqGSIb3DQEBBQUAA4IBAQBGZD1JnMep39KMOhD0iBTmyjhtcnRemckvRask ++pS/CqPwo+M+lPNdxpLU2w9b0QhPnj0yAS/BS1yBjsLGY4DP156k4Q3QOhwsrTmrK ++YOxg0w7DOpkv5g11YLJpHsjSOwg5uIMoefL8mjQK6XOFOmQXHJrUtGulu+fs6FlM ++khGJcW4xYVPK0x/mHvTT8tQaTTkgTdVHObHF5Dyx/F9NMpB3RFguQPk2kT4lJc4i ++Up8T9mLzaxz6xc4wwh8h70Zw81lkGYhX+LRk3sfd/REq9x4QXQNP9t9qU1CgrBzv ++4orzt9cda4r+rleSg2XjWnXzMydE6DuwPVPZlqnLbSYUy660 + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smroot.pem b/test/smime-certs/smroot.pem +index a59eb26..d1a253f 100644 +--- a/test/smime-certs/smroot.pem ++++ b/test/smime-certs/smroot.pem +@@ -1,30 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXAIBAAKBgQDBV1Z/Q5gPF7lojc8pKUdyz5+Jf2B3vs4he6egekugWnoJduki +-9Lnae/JchB/soIX0co3nLc11NuFFlnAWJNMDJr08l5AHAJLYNHevF5l/f9oDQwvZ +-speKh1xpIAJNqCTzVeQ/ZLx6/GccIXV/xDuKIiovqJTPgR5WPkYKaw++lQIDAQAB +-AoGALXnUj5SflJU4+B2652ydMKUjWl0KnL/VjkyejgGV/j6py8Ybaixz9q8Gv7oY +-JDlRqMC1HfZJCFQDQrHy5VJ+CywA/H9WrqKo/Ch9U4tJAZtkig1Cmay/BAYixVu0 +-xBeim10aKF6hxHH4Chg9We+OCuzWBWJhqveNjuDedL/i7JUCQQDlejovcwBUCbhJ +-U12qKOwlaboolWbl7yF3XdckTJZg7+1UqQHZH5jYZlLZyZxiaC92SNV0SyTLJZnS +-Jh5CO+VDAkEA16/pPcuVtMMz/R6SSPpRSIAa1stLs0mFSs3NpR4pdm0n42mu05pO +-1tJEt3a1g7zkreQBf53+Dwb+lA841EkjRwJBAIFmt0DifKDnCkBu/jZh9SfzwsH3 +-3Zpzik+hXxxdA7+ODCrdUul449vDd5zQD5t+XKU61QNLDGhxv5e9XvrCg7kCQH/a +-3ldsVF0oDaxxL+QkxoREtCQ5tLEd1u7F2q6Tl56FDE0pe6Ih6bQ8RtG+g9EI60IN +-U7oTrOO5kLWx5E0q4ccCQAZVgoenn9MhRU1agKOCuM6LT2DxReTu4XztJzynej+8 +-0J93n3ebanB1MlRpn1XJwhQ7gAC8ImaQKLJK5jdJzFc= +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQCyyQXED5HyVWwq ++nXyzmY317yMUJrIfsKvREG2C691dJNHgNg+oq5sjt/fzkyS84AvdOiicAsao4cYL ++DulthaLpbC7msEBhvwAil0FNb5g3ERupe1KuTdUV1UuD/i6S2VoaNXUBBn1rD9Wc ++BBc0lnx/4Wt92eQTI6925pt7ZHPQw2Olp7TQDElyi5qPxCem4uT0g3zbZsWqmmsI ++MXbu+K3dEprzqA1ucKXbxUmZNkMwVs2XCmlLxrRUj8C3/zENtH17HWCznhR/IVcV ++kgIuklkeiDsEhbWvUQumVXR7oPh/CPZAbjGqq5mVueHSHrp7brBVZKHZvoUka28Q ++LWitq1W5AgMBAAECggEASkRnOMKfBeOmQy2Yl6K57eeg0sYgSDnDpd0FINWJ5x9c ++b58FcjOXBodtYKlHIY6QXx3BsM0WaSEge4d+QBi7S+u8r+eXVwNYswXSArDQsk9R ++Bl5MQkvisGciL3pvLmFLpIeASyS/BLJXMbAhU58PqK+jT2wr6idwxBuXivJ3ichu ++ISdT1s2aMmnD86ulCD2DruZ4g0mmk5ffV+Cdj+WWkyvEaJW2GRYov2qdaqwSOxV4 ++Yve9qStvEIWAf2cISQjbnw2Ww6Z5ebrqlOz9etkmwIly6DTbrIneBnoqJlFFWGlF ++ghuzc5RE2w1GbcKSOt0qXH44MTf/j0r86dlu7UIxgQKBgQDq0pEaiZuXHi9OQAOp ++PsDEIznCU1bcTDJewANHag5DPEnMKLltTNyLaBRulMypI+CrDbou0nDr29VOzfXx ++mNvi/c7RttOBOx7kXKvu0JUFKe2oIWRsg0KsyMX7UFMVaHFgrW+8DhQc7HK7URiw ++nitOnA7YwIHRF9BMmcWcLFEYBQKBgQDC6LPbXV8COKO0YCfGXPnE7EZGD/p0Q92Z ++8CoSefphEScSdO1IpxFXG7fOZ4x2GQb9q7D3IvaeKAqNjUjkuyxdB30lIWDBwSWw ++fFgsa2SZwD5P60G/ar50YJr6LiF333aUMDVmC9swFfZERAEmGUz2NTrPWQdIx/lu ++PyDtUR75JQKBgHaoCCJ8vl5SJl1IA5GV4Bo8IoeLTSzsY9d09zMy6BoZcMD1Ix2T ++5S2cXhayoegl9PT6bsYSGHVWFCdJ86ktMI826TcXRzDaCvYhzc9THroJQcnfdbtP ++aHWezkv7fsAmkoPjn75K7ubeo+r7Q5qbkg6a1PW58N8TRXIvkackzaVxAoGBALAq ++qh3U+AHG9dgbrPeyo6KkuCOtX39ks8/mbfCDRZYkbb9V5f5r2tVz3R93IlK/7jyr ++yWimtmde46Lrl33922w+T5OW5qBZllo9GWkUrDn3s5qClcuQjJIdmxYTSfbSCJiK ++NkmE39lHkG5FVRB9f71tgTlWS6ox7TYDYxx83NTtAoGAUJPAkGt4yGAN4Pdebv53 ++bSEpAAULBHntiqDEOu3lVColHuZIucml/gbTpQDruE4ww4wE7dOhY8Q4wEBVYbRI ++vHkSiWpJUvZCuKG8Foh5pm9hU0qb+rbQV7NhLJ02qn1AMGO3F/WKrHPPY8/b9YhQ ++KfvPCYimQwBjVrEnSntLPR0= ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICaTCCAdKgAwIBAgIJAP6VN47boiXRMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDdaFw0xNjA1MTExMzUzMDdaMEQx +-CzAJBgNVBAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRU +-ZXN0IFMvTUlNRSBSU0EgUm9vdDCBnzANBgkqhkiG9w0BAQEFAAOBjQAwgYkCgYEA +-wVdWf0OYDxe5aI3PKSlHcs+fiX9gd77OIXunoHpLoFp6CXbpIvS52nvyXIQf7KCF +-9HKN5y3NdTbhRZZwFiTTAya9PJeQBwCS2DR3rxeZf3/aA0ML2bKXiodcaSACTagk +-81XkP2S8evxnHCF1f8Q7iiIqL6iUz4EeVj5GCmsPvpUCAwEAAaNjMGEwHQYDVR0O +-BBYEFBPPS6e7iS6zOFcXdsabrWhb5e0XMB8GA1UdIwQYMBaAFBPPS6e7iS6zOFcX +-dsabrWhb5e0XMA8GA1UdEwEB/wQFMAMBAf8wDgYDVR0PAQH/BAQDAgEGMA0GCSqG +-SIb3DQEBBQUAA4GBAIECprq5viDvnDbkyOaiSr9ubMUmWqvycfAJMdPZRKcOZczS +-l+L9R9lF3JSqbt3knOe9u6bGDBOTY2285PdCCuHRVMk2Af1f6El1fqAlRUwNqipp +-r68sWFuRqrcRNtk6QQvXfkOhrqQBuDa7te/OVQLa2lGN9Dr2mQsD8ijctatG ++MIIDbjCCAlagAwIBAgIJAMc+8VKBJ/S9MA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MjlaFw0yMzA3MTUxNzI4MjlaMEQx ++CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRU ++ZXN0IFMvTUlNRSBSU0EgUm9vdDCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoC ++ggEBALLJBcQPkfJVbCqdfLOZjfXvIxQmsh+wq9EQbYLr3V0k0eA2D6irmyO39/OT ++JLzgC906KJwCxqjhxgsO6W2FoulsLuawQGG/ACKXQU1vmDcRG6l7Uq5N1RXVS4P+ ++LpLZWho1dQEGfWsP1ZwEFzSWfH/ha33Z5BMjr3bmm3tkc9DDY6WntNAMSXKLmo/E ++J6bi5PSDfNtmxaqaawgxdu74rd0SmvOoDW5wpdvFSZk2QzBWzZcKaUvGtFSPwLf/ ++MQ20fXsdYLOeFH8hVxWSAi6SWR6IOwSFta9RC6ZVdHug+H8I9kBuMaqrmZW54dIe ++untusFVkodm+hSRrbxAtaK2rVbkCAwEAAaNjMGEwHQYDVR0OBBYEFMmRUwpjexZb ++i71E8HaIqSTm5bZsMB8GA1UdIwQYMBaAFMmRUwpjexZbi71E8HaIqSTm5bZsMA8G ++A1UdEwEB/wQFMAMBAf8wDgYDVR0PAQH/BAQDAgEGMA0GCSqGSIb3DQEBBQUAA4IB ++AQAwpIVWQey2u/XoQSMSu0jd0EZvU+lhLaFrDy/AHQeG3yX1+SAOM6f6w+efPvyb ++Op1NPI9UkMPb4PCg9YC7jgYokBkvAcI7J4FcuDKMVhyCD3cljp0ouuKruvEf4FBl ++zyQ9pLqA97TuG8g1hLTl8G90NzTRcmKpmhs18BmCxiqHcTfoIpb3QvPkDX8R7LVt ++9BUGgPY+8ELCgw868TuHh/Cnc67gBtRjBp0sCYVzGZmKsO5f1XdHrAZKYN5mEp0C ++7/OqcDoFqORTquLeycg1At/9GqhDEgxNrqA+YEsPbLGAfsNuXUsXs2ubpGsOZxKt ++Emsny2ah6fU2z7PztrUy/A80 + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa1.pem b/test/smime-certs/smrsa1.pem +index 2cf3148..d0d0b9e 100644 +--- a/test/smime-certs/smrsa1.pem ++++ b/test/smime-certs/smrsa1.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXgIBAAKBgQC6A978j4pmPgUtUQqF+bjh6vdhwGOGZSD7xXgFTMjm88twfv+E +-ixkq2KXSDjD0ZXoQbdOaSbvGRQrIJpG2NGiKAFdYNrP025kCCdh5wF/aEI7KLEm7 +-JlHwXpQsuj4wkMgmkFjL3Ty4Z55aNH+2pPQIa0k+ENJXm2gDuhqgBmduAwIDAQAB +-AoGBAJMuYu51aO2THyeHGwt81uOytcCbqGP7eoib62ZOJhxPRGYjpmuqX+R9/V5i +-KiwGavm63JYUx0WO9YP+uIZxm1BUATzkgkS74u5LP6ajhkZh6/Bck1oIYYkbVOXl +-JVrdENuH6U7nupznsyYgONByo+ykFPVUGmutgiaC7NMVo/MxAkEA6KLejWXdCIEn +-xr7hGph9NlvY9xuRIMexRV/WrddcFfCdjI1PciIupgrIkR65M9yr7atm1iU6/aRf +-KOr8rLZsSQJBAMyyXN71NsDNx4BP6rtJ/LJMP0BylznWkA7zWfGCbAYn9VhZVlSY +-Eu9Gyr7quD1ix7G3kInKVYOEEOpockBLz+sCQQCedyMmKjcQLfpMVYW8uhbAynvW +-h36qV5yXZxszO7nMcCTBsxhk5IfmLv5EbCs3+p9avCDGyoGOeUMg+kC33WORAkAg +-oUIarH4o5+SoeJTTfCzTA0KF9H5U0vYt2+73h7HOnWoHxl3zqDZEfEVvf50U8/0f +-QELDJETTbScBJtsnkq43AkEA38etvoZ2i4FJvvo7R/9gWBHVEcrGzcsCBYrNnIR1 +-SZLRwHEGaiOK1wxMsWzqp7PJwL9z/M8A8DyOFBx3GPOniA== +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvAIBADANBgkqhkiG9w0BAQEFAASCBKYwggSiAgEAAoIBAQDXr9uzB/20QXKC ++xhkfNnJvl2xl1hzdOcrQmAqo+AAAcA/D49ImuJDVQRaK2bcj54XB26i1kXuOrxID ++3/etUb8yudfx8OAVwh8G0xVA4zhr8uXW85W2tBr4v0Lt+W6lSd6Hmfrk4GmE9LTU ++/vzl9HUPW6SZShN1G0nY6oeUXvLi0vasEUKv3a51T6JFYg4c7qt5RCk/w8kwrQ0D ++orQwCdkOPEIiC4b+nPStF12SVm5bx8rbYzioxuY/PdSebvt0APeqgRxSpCxqYnHs ++CoNeHzSrGXcP0COzFeUOz2tdrhmH09JLbGZs4nbojPxMkjpJSv3/ekDG2CHYxXSH ++XxpJstxZAgMBAAECggEASY4xsJaTEPwY3zxLqPdag2/yibBBW7ivz/9p80HQTlXp ++KnbxXj8nNXLjCytAZ8A3P2t316PrrTdLP4ML5lGwkM4MNPhek00GY79syhozTa0i ++cPHVJt+5Kwee/aVI9JmCiGAczh0yHyOM3+6ttIZvvXMVaSl4BUHvJ0ikQBc5YdzL ++s6VM2gCOR6K6n+39QHDI/T7WwO9FFSNnpWFOCHwAWtyBMlleVj+xeZX8OZ/aT+35 ++27yjsGNBftWKku29VDineiQC+o+fZGJs6w4JZHoBSP8TfxP8fRCFVNA281G78Xak ++cEnKXwZ54bpoSa3ThKl+56J6NHkkfRGb8Rgt/ipJYQKBgQD5DKb82mLw85iReqsT ++8bkp408nPOBGz7KYnQsZqAVNGfehM02+dcN5z+w0jOj6GMPLPg5whlEo/O+rt9ze ++j6c2+8/+B4Bt5oqCKoOCIndH68jl65+oUxFkcHYxa3zYKGC9Uvb+x2BtBmYgvDRG ++ew6I2Q3Zyd2ThZhJygUZpsjsbQKBgQDdtNiGTkgWOm+WuqBI1LT5cQfoPfgI7/da ++ZA+37NBUQRe0cM7ddEcNqx7E3uUa1JJOoOYv65VyGI33Ul+evI8h5WE5bupcCEFk ++LolzbMc4YQUlsySY9eUXM8jQtfVtaWhuQaABt97l+9oADkrhA+YNdEu2yiz3T6W+ ++msI5AnvkHQKBgDEjuPMdF/aY6dqSjJzjzfgg3KZOUaZHJuML4XvPdjRPUlfhKo7Q ++55/qUZ3Qy8tFBaTderXjGrJurc+A+LiFOaYUq2ZhDosguOWUA9yydjyfnkUXZ6or ++sbvSoM+BeOGhnezdKNT+e90nLRF6cQoTD7war6vwM6L+8hxlGvqDuRNFAoGAD4K8 ++d0D4yB1Uez4ZQp8m/iCLRhM3zCBFtNw1QU/fD1Xye5w8zL96zRkAsRNLAgKHLdsR ++355iuTXAkOIBcJCOjveGQsdgvAmT0Zdz5FBi663V91o+IDlryqDD1t40CnCKbtRG ++hng/ruVczg4x7OYh7SUKuwIP/UlkNh6LogNreX0CgYBQF9troLex6X94VTi1V5hu ++iCwzDT6AJj63cS3VRO2ait3ZiLdpKdSNNW2WrlZs8FZr/mVutGEcWho8BugGMWST ++1iZkYwly9Xfjnpd0I00ZIlr2/B3+ZsK8w5cOW5Lpb7frol6+BkDnBjbNZI5kQndn ++zQpuMJliRlrq/5JkIbH6SA== ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsTMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDhaFw0xNjA1MTAxMzUzMDhaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBAMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzEwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALoD3vyPimY+BS1RCoX5uOHq92HAY4ZlIPvFeAVMyObzy3B+/4SLGSrYpdIOMPRl +-ehBt05pJu8ZFCsgmkbY0aIoAV1g2s/TbmQIJ2HnAX9oQjsosSbsmUfBelCy6PjCQ +-yCaQWMvdPLhnnlo0f7ak9AhrST4Q0lebaAO6GqAGZ24DAgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFE2vMvKz5jrC7Lbdg68XwZ95iL/QMB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhMUBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQAi +-O3GOkUl646oLnOimc36i9wxZ1tejsqs8vMjJ0Pym6Uq9FE2JoGzJ6OhB1GOsEVmj +-9cQ5UNQcRYL3cqOFtl6f4Dpu/lhzfbaqgmLjv29G1mS0uuTZrixhlyCXjwcbOkNC +-I/+wvHHENYIK5+T/79M9LaZ2Qk4F9MNE1VMljdz9Qw== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzEwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQDXr9uzB/20QXKCxhkfNnJvl2xl1hzdOcrQmAqo+AAAcA/D49ImuJDVQRaK ++2bcj54XB26i1kXuOrxID3/etUb8yudfx8OAVwh8G0xVA4zhr8uXW85W2tBr4v0Lt +++W6lSd6Hmfrk4GmE9LTU/vzl9HUPW6SZShN1G0nY6oeUXvLi0vasEUKv3a51T6JF ++Yg4c7qt5RCk/w8kwrQ0DorQwCdkOPEIiC4b+nPStF12SVm5bx8rbYzioxuY/PdSe ++bvt0APeqgRxSpCxqYnHsCoNeHzSrGXcP0COzFeUOz2tdrhmH09JLbGZs4nbojPxM ++kjpJSv3/ekDG2CHYxXSHXxpJstxZAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBTmjc+lrTQuYx/VBOBGjMvufajvhDAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++dr2IRXcFtlF16kKWs1VTaFIHHNQrfSVHBkhKblPX3f/0s/i3eXgwKUu7Hnb6T3/o ++E8L+e4ioQNhahTLt9ruJNHWA/QDwOfkqM3tshCs2xOD1Cpy7Bd3Dn0YBrHKyNXRK ++WelGp+HetSXJGW4IZJP7iES7Um0DGktLabhZbe25EnthRDBjNnaAmcofHECWESZp ++lEHczGZfS9tRbzOCofxvgLbF64H7wYSyjAe6R8aain0VRbIusiD4tCHX/lOMh9xT ++GNBW8zTL+tV9H1unjPMORLnT0YQ3oAyEND0jCu0ACA1qGl+rzxhF6bQcTUNEbRMu ++9Hjq6s316fk4Ne0EUF3PbA== + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa2.pem b/test/smime-certs/smrsa2.pem +index d41f69c..2f17cb2 100644 +--- a/test/smime-certs/smrsa2.pem ++++ b/test/smime-certs/smrsa2.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICWwIBAAKBgQCwBfryW4Vu5U9wNIDKspJO/N9YF4CcTlrCUyzVlKgb+8urHlSe +-59i5verR9IOCCXkemjOzZ/3nALTGqYZlnEvHp0Rjk+KdKXnKBIB+SRPpeu3LcXMT +-WPgsThPa0UQxedNKG0g6aG+kLhsDlFBCoxd09jJtSpb9jmroJOq0ZYEHLwIDAQAB +-AoGAKa/w4677Je1W5+r3SYoLDnvi5TkDs4D3C6ipKJgBTEdQz+DqB4w/DpZE4551 +-+rkFn1LDxcxuHGRVa+tAMhZW97fwq9YUbjVZEyOz79qrX+BMyl/NbHkf1lIKDo3q +-dWalzQvop7nbzeLC+VmmviwZfLQUbA61AQl3jm4dswT4XykCQQDloDadEv/28NTx +-bvvywvyGuvJkCkEIycm4JrIInvwsd76h/chZ3oymrqzc7hkEtK6kThqlS5y+WXl6 +-QzPruTKTAkEAxD2ro/VUoN+scIVaLmn0RBmZ67+9Pdn6pNSfjlK3s0T0EM6/iUWS +-M06l6L9wFS3/ceu1tIifsh9BeqOGTa+udQJARIFnybTBaIqw/NZ/lA1YCVn8tpvY +-iyaoZ6gjtS65TQrsdKeh/i3HCHNUXxUpoZ3F/H7QtD+6o49ODou+EbVOwQJAVmex +-A2gp8wuJKaINqxIL81AybZLnCCzKJ3lXJ5tUNyLNM/lUbGStktm2Q1zHRQwTxV07 +-jFn7trn8YrtNjzcjYQJAUKIJRt38A8Jw3HoPT+D0WS2IgxjVL0eYGsZX1lyeammG +-6rfnQ3u5uP7mEK2EH2o8mDUpAE0gclWBU9UkKxJsGA== +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQDcYC4tS2Uvn1Z2 ++iDgtfkJA5tAqgbN6X4yK02RtVH5xekV9+6+eTt/9S+iFAzAnwqR/UB1R67ETrsWq ++V8u9xLg5fHIwIkmu9/6P31UU9cghO7J1lcrhHvooHaFpcXepPWQacpuBq2VvcKRD ++lDfVmdM5z6eS3dSZPTOMMP/xk4nhZB8mcw27qiccPieS0PZ9EZB63T1gmwaK1Rd5 ++U94Pl0+zpDqhViuXmBfiIDWjjz0BzHnHSz5Rg4S3oXF1NcojhptIWyI0r7dgn5J3 ++NxC4kgKdjzysxo6iWd0nLgz7h0jUdj79EOis4fg9G4f0EFWyQf7iDxGaA93Y9ePB ++Jv5iFZVZAgMBAAECggEBAILIPX856EHb0KclbhlpfY4grFcdg9LS04grrcTISQW1 ++J3p9nBpZ+snKe6I8Yx6lf5PiipPsSLlCliHiWpIzJZVQCkAQiSPiHttpEYgP2IYI ++dH8dtznkdVbLRthZs0bnnPmpHCpW+iqpcYJ9eqkz0cvUNUGOjjWmwWmoRqwp/8CW ++3S1qbkQiCh0Mk2fQeGar76R06kXQ9MKDEj14zyS3rJX+cokjEoMSlH8Sbmdh2mJz ++XlNZcvqmeGJZwQWgbVVHOMUuZaKJiFa+lqvOdppbqSx0AsCRq6vjmjEYQEoOefYK ++3IJM9IvqW5UNx0Cy4kQdjhZFFwMO/ALD3QyF21iP4gECgYEA+isQiaWdaY4UYxwK ++Dg+pnSCKD7UGZUaCUIv9ds3CbntMOONFe0FxPsgcc4jRYQYj1rpQiFB8F11+qXGa ++P/IHcnjr2+mTrNY4I9Bt1Lg+pHSS8QCgzeueFybYMLaSsXUo7tGwpvw6UUb6/YWI ++LNCzZbrCLg1KZjGODhhxtvN45ZkCgYEA4YNSe+GMZlxgsvxbLs86WOm6DzJUPvxN ++bWmni0+Oe0cbevgGEUjDVc895uMFnpvlgO49/C0AYJ+VVbStjIMgAeMnWj6OZoSX ++q49rI8KmKUxKgORZiiaMqGWQ7Rxv68+4S8WANsjFxoUrE6dNV3uYDIUsiSLbZeI8 ++38KVTcLohcECgYEAiOdyWHGq0G4xl/9rPUCzCMsa4velNV09yYiiwBZgVgfhsawm ++hQpOSBZJA60XMGqkyEkT81VgY4UF4QLLcD0qeCnWoXWVHFvrQyY4RNZDacpl87/t ++QGO2E2NtolL3umesa+2TJ/8Whw46Iu2llSjtVDm9NGiPk5eA7xPPf1iEi9kCgYAb ++0EmVE91wJoaarLtGS7LDkpgrFacEWbPnAbfzW62UENIX2Y1OBm5pH/Vfi7J+vHWS ++8E9e0eIRCL2vY2hgQy/oa67H151SkZnvQ/IP6Ar8Xvd1bDSK8HQ6tMQqKm63Y9g0 ++KDjHCP4znOsSMnk8h/bZ3HcAtvbeWwftBR/LBnYNQQKBgA1leIXLLHRoX0VtS/7e ++y7Xmn7gepj+gDbSuCs5wGtgw0RB/1z/S3QoS2TCbZzKPBo20+ivoRP7gcuFhduFR ++hT8V87esr/QzLVpjLedQDW8Xb7GiO3BsU/gVC9VcngenbL7JObl3NgvdreIYo6+n ++yrLyf+8hjm6H6zkjqiOkHAl+ ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsUMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDhaFw0xNjA1MTAxMzUzMDhaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBBMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzIwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALAF+vJbhW7lT3A0gMqykk7831gXgJxOWsJTLNWUqBv7y6seVJ7n2Lm96tH0g4IJ +-eR6aM7Nn/ecAtMaphmWcS8enRGOT4p0pecoEgH5JE+l67ctxcxNY+CxOE9rRRDF5 +-00obSDpob6QuGwOUUEKjF3T2Mm1Klv2Oaugk6rRlgQcvAgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFIL/u+mEvaw7RuKLRuElfVkxSQjYMB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhMkBvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQC2 +-rXR5bm/9RtOMQPleNpd3y6uUX3oy+0CafK5Yl3PMnItjjnKJ0l1/DbLbDj2twehe +-ewaB8CROcBCA3AMLSmGvPKgUCFMGtWam3328M4fBHzon5ka7qDXzM+imkAly/Yx2 +-YNdR/aNOug+5sXygHmTSKqiCpQjOIClzXoPVVeEVHw== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzIwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQDcYC4tS2Uvn1Z2iDgtfkJA5tAqgbN6X4yK02RtVH5xekV9+6+eTt/9S+iF ++AzAnwqR/UB1R67ETrsWqV8u9xLg5fHIwIkmu9/6P31UU9cghO7J1lcrhHvooHaFp ++cXepPWQacpuBq2VvcKRDlDfVmdM5z6eS3dSZPTOMMP/xk4nhZB8mcw27qiccPieS ++0PZ9EZB63T1gmwaK1Rd5U94Pl0+zpDqhViuXmBfiIDWjjz0BzHnHSz5Rg4S3oXF1 ++NcojhptIWyI0r7dgn5J3NxC4kgKdjzysxo6iWd0nLgz7h0jUdj79EOis4fg9G4f0 ++EFWyQf7iDxGaA93Y9ePBJv5iFZVZAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBT0arpyYMHXDPVL7MvzE+lx71L7sjAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++I8nM42am3aImkZyrw8iGkaGhKyi/dfajSWx6B9izBUh+3FleBnUxxOA+mn7M8C47 ++Ne18iaaWK8vEux9KYTIY8BzXQZL1AuZ896cXEc6bGKsME37JSsocfuB5BIGWlYLv ++/ON5/SJ0iVFj4fAp8z7Vn5qxRJj9BhZDxaO1Raa6cz6pm0imJy9v8y01TI6HsK8c ++XJQLs7/U4Qb91K+IDNX/lgW3hzWjifNpIpT5JyY3DUgbkD595LFV5DDMZd0UOqcv ++6cyN42zkX8a0TWr3i5wu7pw4k1oD19RbUyljyleEp0DBauIct4GARdBGgi5y1H2i ++NzYzLAPBkHCMY0Is3KKIBw== + -----END CERTIFICATE----- +diff --git a/test/smime-certs/smrsa3.pem b/test/smime-certs/smrsa3.pem +index c8cbe55..14c27f6 100644 +--- a/test/smime-certs/smrsa3.pem ++++ b/test/smime-certs/smrsa3.pem +@@ -1,31 +1,49 @@ +------BEGIN RSA PRIVATE KEY----- +-MIICXAIBAAKBgQC6syTZtZNe1hRScFc4PUVyVLsr7+C1HDIZnOHmwFoLayX6RHwy +-ep/TkdwiPHnemVLuwvpSjLMLZkXy/J764kSHJrNeVl3UvmCVCOm40hAtK1+F39pM +-h8phkbPPD7i+hwq4/Vs79o46nzwbVKmzgoZBJhZ+codujUSYM3LjJ4aq+wIDAQAB +-AoGAE1Zixrnr3bLGwBMqtYSDIOhtyos59whImCaLr17U9MHQWS+mvYO98if1aQZi +-iQ/QazJ+wvYXxWJ+dEB+JvYwqrGeuAU6He/rAb4OShG4FPVU2D19gzRnaButWMeT +-/1lgXV08hegGBL7RQNaN7b0viFYMcKnSghleMP0/q+Y/oaECQQDkXEwDYJW13X9p +-ijS20ykWdY5lLknjkHRhhOYux0rlhOqsyMZjoUmwI2m0qj9yrIysKhrk4MZaM/uC +-hy0xp3hdAkEA0Uv/UY0Kwsgc+W6YxeypECtg1qCE6FBib8n4iFy/6VcWqhvE5xrs +-OdhKv9/p6aLjLneGd1sU+F8eS9LGyKIbNwJBAJPgbNzXA7uUZriqZb5qeTXxBDfj +-RLfXSHYKAKEULxz3+JvRHB9SR4yHMiFrCdExiZrHXUkPgYLSHLGG5a4824UCQD6T +-9XvhquUARkGCAuWy0/3Eqoihp/t6BWSdQ9Upviu7YUhtUxsyXo0REZB7F4pGrJx5 +-GlhXgFaewgUzuUHFzlMCQCzJMMWslWpoLntnR6sMhBMhBFHSw+Y5CbxBmFrdtSkd +-VdtNO1VuDCTxjjW7W3Khj7LX4KZ1ye/5jfAgnnnXisc= +------END RSA PRIVATE KEY----- ++-----BEGIN PRIVATE KEY----- ++MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQCyK+BTAOJKJjji ++OhY60NeZjzGGZxEBfCm62n0mwkzusW/V/e63uwj6uOVCFoVBz5doMf3M6QIS2jL3 ++Aw6Qs5+vcuLA0gHrqIwjYQz1UZ5ETLKLKbQw6YOIVfsFSTxytUVpfcByrubWiLKX ++63theG1/IVokDK/9/k52Kyt+wcCjuRb7AJQFj2OLDRuWm/gavozkK103gQ+dUq4H ++XamZMtTq1EhQOfc0IUeCOEL6xz4jzlHHfzLdkvb7Enhav2sXDfOmZp/DYf9IqS7l ++vFkkINPVbYFBTexaPZlFwmpGRjkmoyH/w+Jlcpzs+w6p1diWRpaSn62bbkRN49j6 ++L2dVb+DfAgMBAAECggEAciwDl6zdVT6g/PbT/+SMA+7qgYHSN+1koEQaJpgjzGEP ++lUUfj8TewCtzXaIoyj9IepBuXryBg6snNXpT/w3bqgYon/7zFBvxkUpDj4A5tvKf ++BuY2fZFlpBvUu1Ju1eKrFCptBBBoA9mc+BUB/ze4ktrAdJFcxZoMlVScjqGB3GdR ++OHw2x9BdWGCJBhiu9VHhAAb/LVWi6xgDumYSWZwN2yovg+7J91t5bsENeBRHycK+ ++i5dNFh1umIK9N0SH6bpHPnLHrCRchrQ6ZRRxL4ZBKA9jFRDeI7OOsJuCvhGyJ1se ++snsLjr/Ahg00aiHCcC1SPQ6pmXAVBCG7hf4AX82V4QKBgQDaFDE+Fcpv84mFo4s9 ++wn4CZ8ymoNIaf5zPl/gpH7MGots4NT5+Ns+6zzJQ6TEpDjTPx+vDaabP7QGXwVZn ++8NAHYvCQK37b+u9HrOt256YYRDOmnJFSbsJdmqzMEzpTNmQ8GuI37cZCS9CmSMv+ ++ab/plcwuv0cJRSC83NN2AFyu1QKBgQDRJzKIBQlpprF9rA0D5ZjLVW4OH18A0Mmm ++oanw7qVutBaM4taFN4M851WnNIROyYIlkk2fNgW57Y4M8LER4zLrjU5HY4lB0BMX ++LQWDbyz4Y7L4lVnnEKfQxWFt9avNZwiCxCxEKy/n/icmVCzc91j9uwKcupdzrN6E ++yzPd1s5y4wKBgQCkJvzmAdsOp9/Fg1RFWcgmIWHvrzBXl+U+ceLveZf1j9K5nYJ7 ++2OBGer4iH1XM1I+2M4No5XcWHg3L4FEdDixY0wXHT6Y/CcThS+015Kqmq3fBmyrc ++RNjzQoF9X5/QkSmkAIx1kvpgXtcgw70htRIrToGSUpKzDKDW6NYXhbA+PQKBgDJK ++KH5IJ8E9kYPUMLT1Kc4KVpISvPcnPLVSPdhuqVx69MkfadFSTb4BKbkwiXegQCjk ++isFzbeEM25EE9q6EYKP+sAm+RyyJ6W0zKBY4TynSXyAiWSGUAaXTL+AOqCaVVZiL ++rtEdSUGQ/LzclIT0/HLV2oTw4KWxtTdc3LXEhpNdAoGBAM3LckiHENqtoeK2gVNw ++IPeEuruEqoN4n+XltbEEv6Ymhxrs6T6HSKsEsLhqsUiIvIzH43KMm45SNYTn5eZh ++yzYMXLmervN7c1jJe2Y2MYv6hE+Ypj1xGW4w7s8WNKmVzLv97beisD9AZrS7sXfF ++RvOAi5wVkYylDxV4238MAZIq ++-----END PRIVATE KEY----- + -----BEGIN CERTIFICATE----- +-MIICizCCAfSgAwIBAgIJAMtotfHYdEsVMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV +-BAYTAlVLMRYwFAYDVQQKEw1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDExRUZXN0IFMv +-TUlNRSBSU0EgUm9vdDAeFw0wODAyMjIxMzUzMDlaFw0xNjA1MTAxMzUzMDlaMEUx ++MIIDbDCCAlSgAwIBAgIJANk5lu6mSyBCMA0GCSqGSIb3DQEBBQUAMEQxCzAJBgNV ++BAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR0wGwYDVQQDDBRUZXN0IFMv ++TUlNRSBSU0EgUm9vdDAeFw0xMzA3MTcxNzI4MzBaFw0yMzA1MjYxNzI4MzBaMEUx + CzAJBgNVBAYTAlVLMRYwFAYDVQQKDA1PcGVuU1NMIEdyb3VwMR4wHAYDVQQDDBVU +-ZXN0IFMvTUlNRSBFRSBSU0EgIzMwgZ8wDQYJKoZIhvcNAQEBBQADgY0AMIGJAoGB +-ALqzJNm1k17WFFJwVzg9RXJUuyvv4LUcMhmc4ebAWgtrJfpEfDJ6n9OR3CI8ed6Z +-Uu7C+lKMswtmRfL8nvriRIcms15WXdS+YJUI6bjSEC0rX4Xf2kyHymGRs88PuL6H +-Crj9Wzv2jjqfPBtUqbOChkEmFn5yh26NRJgzcuMnhqr7AgMBAAGjgYMwgYAwHQYD +-VR0OBBYEFDsSFjNtYZzd0tTHafNS7tneQQj6MB8GA1UdIwQYMBaAFBPPS6e7iS6z +-OFcXdsabrWhb5e0XMAwGA1UdEwEB/wQCMAAwDgYDVR0PAQH/BAQDAgXgMCAGA1Ud +-EQQZMBeBFXNtaW1lcnNhM0BvcGVuc3NsLm9yZzANBgkqhkiG9w0BAQUFAAOBgQBE +-tUDB+1Dqigu4p1xtdq7JRK6S+gfA7RWmhz0j2scb2zhpS12h37JLHsidGeKAzZYq +-jUjOrH/j3xcV5AnuJoqImJaN23nzzxtR4qGGX2mrq6EtObzdEGgCUaizsGM+0slJ +-PYxcy8KeY/63B1BpYhj2RjGkL6HrvuAaxVORa3acoA== ++ZXN0IFMvTUlNRSBFRSBSU0EgIzMwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEK ++AoIBAQCyK+BTAOJKJjjiOhY60NeZjzGGZxEBfCm62n0mwkzusW/V/e63uwj6uOVC ++FoVBz5doMf3M6QIS2jL3Aw6Qs5+vcuLA0gHrqIwjYQz1UZ5ETLKLKbQw6YOIVfsF ++STxytUVpfcByrubWiLKX63theG1/IVokDK/9/k52Kyt+wcCjuRb7AJQFj2OLDRuW ++m/gavozkK103gQ+dUq4HXamZMtTq1EhQOfc0IUeCOEL6xz4jzlHHfzLdkvb7Enha ++v2sXDfOmZp/DYf9IqS7lvFkkINPVbYFBTexaPZlFwmpGRjkmoyH/w+Jlcpzs+w6p ++1diWRpaSn62bbkRN49j6L2dVb+DfAgMBAAGjYDBeMAwGA1UdEwEB/wQCMAAwDgYD ++VR0PAQH/BAQDAgXgMB0GA1UdDgQWBBQ6CkW5sa6HrBsWvuPOvMjyL5AnsDAfBgNV ++HSMEGDAWgBTJkVMKY3sWW4u9RPB2iKkk5uW2bDANBgkqhkiG9w0BAQUFAAOCAQEA ++JhcrD7AKafVzlncA3cZ6epAruj1xwcfiE+EbuAaeWEGjoSltmevcjgoIxvijRVcp ++sCbNmHJZ/siQlqzWjjf3yoERvLDqngJZZpQeocMIbLRQf4wgLAuiBcvT52wTE+sa ++VexeETDy5J1OW3wE4A3rkdBp6hLaymlijFNnd5z/bP6w3AcIMWm45yPm0skM8RVr ++O3UstEFYD/iy+p+Y/YZDoxYQSW5Vl+NkpGmc5bzet8gQz4JeXtH3z5zUGoDM4XK7 ++tXP3yUi2eecCbyjh/wgaQiVdylr1Kv3mxXcTl+cFO22asDkh0R/y72nTCu5fSILY ++CscFo2Z2pYROGtZDmYqhRw== + -----END CERTIFICATE----- -- GitLab From 73fdfc638a0da3bea0ac53e15f29b480f2138b15 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Sun, 15 May 2016 16:41:57 +0200 Subject: [PATCH 0859/2403] Fix checksum after updating patch --- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index c013f5f3e6..5df9e5efff 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -32,7 +32,7 @@ patches = [ checksums = [ '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz - 'e5bfc115b9013b87a294a3bd84db02ed', # Score-P-2.0.1_fix_score_configure.patch + '557b3a292591740271be7f336d5b7473', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ -- GitLab From 83129f4445b05f5dbc7a4d20468b63f9512ab4b0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 15 May 2016 22:03:37 +0100 Subject: [PATCH 0860/2403] Update sympy to 1.0 and add patch to fix Unicode-related test failure --- .../mpmath-0.19-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ .../sympy-1.0-foss-2016a-Python-2.7.11.eb | 33 ++++++++++++++++++ .../s/sympy/sympy-1.0_tests-unicode.patch | 19 +++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6602e3fb19 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..4c408ec5d7 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#Patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch new file mode 100644 index 0000000000..a17da8977f --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -0,0 +1,19 @@ +Fix for Unicode error that causes one of the tests to fail + +For reference, see +http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte +and http://nedbatchelder.com/text/unipain/unipain.html + + +diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py +--- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 ++++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 +@@ -164,7 +164,7 @@ + except CalledProcessError as e: + raise CodeWrapError( + "Error while executing command: %s. Command output is:\n%s" % ( +- " ".join(command), e.output.decode())) ++ " ".join(command), e.output.decode('ascii', 'ignore'))) + if not self.quiet: + print(retoutput) + -- GitLab From a7995c806ecdb67cbbe8041d8cc571bdfe8f6202 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 10:37:37 +0800 Subject: [PATCH 0861/2403] drop unnecessary comments --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb index 049507e41f..d13b10cfef 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9.eb @@ -20,9 +20,6 @@ configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' configopts += '--with-fft-flavor=fftw3-mkl ' configopts += '--with-fft-libs="$LIBFFT"' -# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? -# eb --try-amend can be used to install those variants from the same easyconfig file... - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], -- GitLab From 5fdcf6ce002aa13e8815c42b46820dd8d6356035 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 10:39:38 +0800 Subject: [PATCH 0862/2403] rename variant --- ....9_libxc.eb => ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb => ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb} (97%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb similarity index 97% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb index 113a1ca853..cfbc03496c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9_libxc.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'ABINIT' version = "7.10.5" -versionsuffix = "_libxc" +versionsuffix = "-libxc" homepage = 'http://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, -- GitLab From f97d2048941547a82f3bad4098882834786b172c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 12:15:41 +0800 Subject: [PATCH 0863/2403] using updated easyblock --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 81 ++++++++++++------- .../QuantumESPRESSO-5.3.0_yambo-fixes.patch | 49 +++++++++++ 2 files changed, 101 insertions(+), 29 deletions(-) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 91045a89e8..a8b352aa0f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -1,42 +1,65 @@ -easyblock = 'ConfigureMake' - name = 'QuantumESPRESSO' version = '5.3.0' -homepage = 'http://www.quantum-espresso.org' -description = """Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the nanoscale. - It is based on density-functional theory, plane waves, and pseudopotentials.""" +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -source_urls = ['http://qe-forge.org/gf/download/frsrelease/204/912/'] -sources = ['espresso-%(version)s.tar.gz'] -checksums = ['6848fcfaeb118587d6be36bd10b7f2c3'] +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + # 'plumed-1.3-qe-r11758.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.1-rev61.tgz', + 'xspectra-%(version)s.tar.gz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/204/912/', # espresso-5.3.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz +] -configopts = 'DFLAGS="-D__INTEL -D__MPI -D__PARA -D__DFTI -D__SCALAPACK" ' -configopts += 'FFT_LIBS="$LIBFFT" --with-scalapack=intel ' -configopts += '--prefix=%(installdir)s/bin' +patches = [ + 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', +] -buildopts = 'all' +# source checksums +checksums = [ + '6848fcfaeb118587d6be36bd10b7f2c3', # espresso-5.3.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + 'e713f74b78a04600265e697ca346bea1', # atomic-5.3.0.tar.gz + '91157da66570deb4e7a353a23621a39f', # neb-5.3.0.tar.gz + '994c89e72b5500bceb44dada7134cc12', # PHonon-5.3.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '897753893dc46502de24b81929694ee1', # pwcond-5.3.0.tar.gz + 'ac9d86386f2b2d28a6b00c902668669b', # tddfpt-5.3.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + 'fc7d9d80e00185afcab44307d3b70a65', # xspectra-5.3.0.tar.gz +] -parallel = 1 +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +buildopts = 'all w90 want yambo xspectra' # plumed -sanity_check_paths = { - 'files': ['bin/' + prog for prog in ['average.x', 'bands.x', 'bgw2pw.x', 'cppp.x', - 'cp.x', 'd3.x', 'dist.x', 'dos.x', 'dynmat.x', 'epsilon.x', 'ev.x', 'fd_ef.x', - 'fd_ifc.x', 'fd.x', 'fqha.x', 'fs.x', 'generate_rVV10_kernel_table.x', - 'generate_vdW_kernel_table.x', 'importexport_binary.x', 'initial_state.x', - 'iotk_print_kinds.x', 'iotk.x', 'kpoints.x', 'lambda.x', 'ld1.x', - 'manypw.x', 'matdyn.x', 'molecularpdos.x', 'neb.x', 'path_interpolation.x', - 'phcg.x', 'ph.x', 'plan_avg.x', 'plotband.x', 'plotproj.x', 'plotrho.x', - 'pmw.x', 'pp.x', 'projwfc.x', 'pw2bgw.x', 'pw2gw.x', 'pw2wannier90.x', - 'pwcond.x', 'pw_export.x', 'pwi2xsf.x', 'pw.x', 'q2qstar.x', 'q2r.x', - 'q2trans_fd.x', 'q2trans.x', 'spectra_manipulation.x', 'sumpdos.x', - 'turbo_davidson.x', 'turbo_eels.x', 'turbo_lanczos.x', 'turbo_spectrum.x', - 'wannier_ham.x', 'wannier_plot.x', 'wfck2r.x', 'wfdd.x', 'xspectra.x']], - 'dirs': [], -} +# parallel build tends to fail +parallel = 1 moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch new file mode 100644 index 0000000000..da11a59d73 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch @@ -0,0 +1,49 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +--- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 ++++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 +@@ -6077,7 +6077,7 @@ + UFFLAGS="-O0 -mtune=native" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -6116,7 +6116,7 @@ + UFFLAGS="-O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6159,7 +6159,7 @@ + SYSFLAGS="-O3 -w" + UFFLAGS="-O0 -w" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6212,7 +6212,7 @@ + SYSFLAGS="-O3 -w -tpp2" + UFFLAGS="-O0 -w -tpp2" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -7316,7 +7316,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; -- GitLab From a36025898df5b11b7838e507cc0b105d5fcb5cc5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 12:16:43 +0800 Subject: [PATCH 0864/2403] remove unnecessary comments --- .../a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb index cfbc03496c..9651451f5d 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.5-intel-2016.02-GCC-4.9-libxc.eb @@ -21,9 +21,6 @@ configopts = '--with-fc-vendor=intel --with-linalg-flavor=mkl --enable-mpi ' configopts += '--with-fft-flavor=fftw3-mkl ' configopts += '--with-fft-libs="$LIBFFT" ' -# there are variants (e.g. --with-dft-flavor), but is an easyconfig file needed for all? -# eb --try-amend can be used to install those variants from the same easyconfig file... - # libxc variant configopts += '--with-dft-flavor=libxc ' -- GitLab From 57d47457ef583e6ad0755d3a66a3f9cf65bcdff0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 06:00:04 +0100 Subject: [PATCH 0865/2403] Fix typo in sanity check macros --- .../easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb index 4c408ec5d7..6ab91f87e3 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -27,7 +27,7 @@ runtest = 'python setup.py test' sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)-py%(pyshortver)s.egg/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], } moduleclass = 'math' -- GitLab From f5c549eb5ae373a5dc0a957c31cada899a2f7a05 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 17:00:40 +0800 Subject: [PATCH 0866/2403] add 5.4.0 files --- ...tumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 66 +++++++++++++++++++ .../QuantumESPRESSO-5.4.0_yambo-fixes.patch | 49 ++++++++++++++ 2 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..08ae4e6988 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,66 @@ +name = 'QuantumESPRESSO' +version = '5.4.0' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + #'plumed-1.3-qe-r11758.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.1-rev61.tgz', + 'xspectra-%(version)s.tar.gz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz +] + +patches = [ + 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', +] + +# source checksums +checksums = [ + '8bb78181b39bd084ae5cb7a512c1cfe7', # espresso-5.4.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + '24dc0d8bf5cf4eb4dc38e1c18a80b3ee', # atomic-5.4.0.tar.gz + '254f929259fb06036b78c493cf18e5d6', # neb-5.4.0.tar.gz + 'f641fe9dcf0ec8f1e47d74e3c7c39705', # PHonon-5.4.0.tar.gz + #'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '31c1cd8cd76752833a9205d456093d0a', # pwcond-5.4.0.tar.gz + '2101533a627644ef467b60d400977eab', # tddfpt-5.4.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + '95080929c87389cd15cf765048cfc9d2', # xspectra-5.4.0.tar.gz +] + +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# plumed excluded due to not finding the source package +buildopts = 'all w90 want yambo xspectra' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch new file mode 100644 index 0000000000..da11a59d73 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch @@ -0,0 +1,49 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +--- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 ++++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 +@@ -6077,7 +6077,7 @@ + UFFLAGS="-O0 -mtune=native" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -6116,7 +6116,7 @@ + UFFLAGS="-O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6159,7 +6159,7 @@ + SYSFLAGS="-O3 -w" + UFFLAGS="-O0 -w" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6212,7 +6212,7 @@ + SYSFLAGS="-O3 -w -tpp2" + UFFLAGS="-O0 -w -tpp2" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -7316,7 +7316,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; -- GitLab From 7a6a7ba89c52be30e19e5546fafb96bbaf8975d2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:05:45 +0100 Subject: [PATCH 0867/2403] Add authorship info to the patch for unicode --- easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch index a17da8977f..87e12a3b40 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -4,6 +4,10 @@ For reference, see http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte and http://nedbatchelder.com/text/unipain/unipain.html +Patch created by: + +Adam Huffman +The Francis Crick Institute diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py --- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 -- GitLab From 225b21792ef7ff57a6e5ad60686d569277128ca1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:10:26 +0100 Subject: [PATCH 0868/2403] Add link for upstream versioning --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index 110e6af4ca..b0297d5d90 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -6,6 +6,7 @@ easyblock = 'Tarball' name = 'annovar' # Unconventional version is taken from the upstream site +# http://annovar.openbioinformatics.org/en/latest/user-guide/download/ version = '2016Feb01' versionsuffix = '-Perl-%(perlver)s' -- GitLab From 207aaede2ddbdade821faaf9b554a34644dc2013 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 16 May 2016 10:19:38 +0100 Subject: [PATCH 0869/2403] Fix merge conflict from annovar --- .../a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index 2ab347b203..e14e022891 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -19,13 +19,9 @@ toolchain = {'name': 'foss', 'version': '2016a'} # Registration required for download # http://www.openbioinformatics.org/annovar/annovar_download_form.php -<<<<<<< HEAD # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['2b26e514c54a847bfdcf4ce57e43f95c'] -======= -sources = ['%(name)s.latest.tar.gz'] ->>>>>>> annovar dependencies = [('Perl', '5.22.1')] -- GitLab From 3b931d441a287ca1d2be5b399c87ce6bcc344fc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 May 2016 12:26:15 +0200 Subject: [PATCH 0870/2403] add back patch in OpenSSL easyconfig --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb index 91cb41c8eb..4428c9a63c 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1k-intel-2015a.eb @@ -13,6 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', 'OpenSSL-1.0.x_fix-tests-certs.patch', ] -- GitLab From 922ad368943477ba75a831f18969b85f49fc7bcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 May 2016 12:27:10 +0200 Subject: [PATCH 0871/2403] remove unneeded patch in OpenSSL easyconfig --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index c4f94fabf9..85aca68623 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -12,10 +12,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-1.0.x_fix-tests-certs.patch', -] +patches = ['OpenSSL-1.0.x_fix-tests-certs.patch'] dependencies = [('zlib', '1.2.8')] -- GitLab From e73986eef546f8d93b0d26664c74db6bab061803 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 10:25:48 +0200 Subject: [PATCH 0872/2403] bump version to 2.8.0 and update release notes --- RELEASE_NOTES | 71 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 70 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b5c225454e..cb97cc538e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,75 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 5,580 easyconfig files, for 862 different software packages, -34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,063 easyconfig files, for 931 different software packages, +36 different (compiler) toolchains, 12 software bundles and 1 meta-package. + + +v2.8.0 (May 18th 2016) +---------------------- + +feature + bugfix release +- added example easyconfig files for 69 new software packages: + ALPS (#2888), annovar (#3010), BayeScEnv (#2765), BayesAss (#2870), BerkeleyGW (#2925), Blitz++ (#2784, #3004), + bam-readcount (#2850), Commet (#2938), CrossTalkZ (#2939), cuDNN (#2882), DBus (#2855), DFT-D3 (#2107), + DIAL (#3056), dask (#2885), dbus-glib (#2855), FFLAS-FFPACK (#2793), FLAC (#2824), FLANN (#3015, #3029), + FLEUR (#3043), GConf (#2855), GROMOS++ (#1297), GST-plugins-base (#2855), GStreamer (#2855), GTOOL (#2805), + Givaro (#2793), gdist (#2935), gromosXX (#1297), HISAT2 (#2809), i-PI (#2940), Kraken (#3037, #3041), LAME (#2823), + LASTZ (#3002), LinBox (#2793), Loki (#2839), libQGLViewer (#2923, #3008), libXxf86vm (#2855), + MDSplus (#2787, #2838, #3027), MRIcron (#2831), Mawk (#2732), minieigen (#2839), mpmath (#3058), NBO (#3047, 3048), + NGS (#2803), NGS-Python (#2810), ncbi-vdb (#2808), OptiX (#2795), PCL (#3024), PEAR (#2731), PLplot (#2990), + Postgres-XL (#2891), PyGTS (#2969), RSeQC (#2788), Rust (#2920, #2943), rainbow (#2730), SHAPEIT (#2806), + SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665), + travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855), + Yade (#2839), Yambo (#2932) +- add test configuration for Travis (#2942, #2944, #2954) +- added easyconfigs for new PGI-based toolchains: pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044) +- added new easyconfigs for existing toolchains: + foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, + LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8 +- various other enhancements, including: + - enhance ORCA easyconfig for compatibility with SLURM (#1819) + - enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764) + - clean up binutils easyconfigs to use binutils easyblock (#3006) + - add include/GraphicsMagick to CPATH in GraphicsMagick easyconfigs (#3034) + - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) +- various bug fixes, including: + - fix perl extensions download urls (#2738) + - add Autconf as build dep for GCCcore (#2772) + - fix versions of extensions in Bioconductor 3.2 bundles (#2769) + - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) + - use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812) + - add zlib as explicit dep in Tk easyconfigs (#2815) + - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816) + - fix homepage and description in Pygments easyconfigs (#2822) + - include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827) + - consistently use XORG_*_SOURCE constants (#2829, #2830) + - update source URLs in ScientificPython easyconfig files (#2847) + - use XORG_LIB_SOURCE in libICE/libSM easyconfigs (#2848) + - add checksums in SuiteSparse easyconfigs (#2849) + - fix build deps for GObject-Introspection (#2852) + - correctly specify Perl location in git easyconfig (#2866) + - fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880) + - fix Perl dependency in worker, it required non-standard Perl modules (#2884) + - add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887) + - fix download URL for packmol (#2902) + - drop usempi toolchain in numexpr easyconfigs, not needed (#2937) + - fix use of resolve_dependencies in tests according to changes in framework (#2952) + - add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (#2967) + - add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (#2971) + - add xproto build dependency for makedepend v1.0.5 (#2982) + - disable parallel build for Doxygen (#2986) + - fix source URLs for FreezeThaw and Tie::Function extensions for Perl v5.22.1 (#2988) + - add sed command in worker easyconfig files to fix module_path in conf/worker.conf (#2997, #3000) + - drop toolchainopts from Eigen easyconfigs, since it is headers-only (#3025) + - clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ (#3036) + - use %(pyshortver)s template rather than hardcoding 2.7 in VTK easyconfigs (#3052) + - correct install location of OpenCV Python bindings (#3054) + - include XZ as dependency for libunwind (#3055) + - add patch to fix broken OpenSSL tests due to expired certificates (#3057) + v2.7.0 (March 20th 2016) ------------------------ diff --git a/setup.py b/setup.py index cf1d254d29..d2fef70086 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0.dev0' +VERSION = '2.8.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 1e705738e9567b5237324ca729f7646b1aedbadd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 14:06:18 +0200 Subject: [PATCH 0873/2403] fix build status badges in README, use the ones from Travis --- README.rst | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/README.rst b/README.rst index becdc63ccb..b6fcf302e9 100644 --- a/README.rst +++ b/README.rst @@ -34,22 +34,12 @@ Related Python packages: *Build status overview:* -* **master** branch *(Python 2.4, Python 2.6, Python 2.7)* +* **master** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python24/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=master + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master/ +* **develop** branch: - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_master-python27/ - -* **develop** branch *(Python 2.4, Python 2.6, Python 2.7)* - - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python24/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop/ - .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/badge/icon - :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-easyconfigs_unit-test_hpcugent_develop-python27/ + .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=develop + :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches -- GitLab From 98ab18eb46e99ecef1396cfa001cfbb94a1c7859 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 18:02:56 +0200 Subject: [PATCH 0874/2403] fix broken link to VSC website --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index cf1d254d29..6315d80947 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/__init__.py b/test/__init__.py index 856f7e4178..e44e0c6e58 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2d23e93e64..c92b7c5d93 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -4,7 +4,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 79a1fb0d08..18f087e264 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -5,7 +5,7 @@ # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), # with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -- GitLab From c2c6064c86b5a9c18bc8eaf6db4bffc0981b2996 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 18:40:55 +0200 Subject: [PATCH 0875/2403] include #2927,#3061,#3062 in release notes --- RELEASE_NOTES | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cb97cc538e..55f4ecd971 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,063 easyconfig files, for 931 different software packages, -36 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,064 easyconfig files, for 931 different software packages, +37 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.8.0 (May 18th 2016) @@ -24,8 +24,9 @@ feature + bugfix release SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665), travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855), Yade (#2839), Yambo (#2932) -- add test configuration for Travis (#2942, #2944, #2954) -- added easyconfigs for new PGI-based toolchains: pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044) +- add test configuration for Travis (#2942, #2944, #2954, #3061) +- added easyconfigs for new PGI-based toolchains + - pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044), CrayPGI/2016.04 (#2927) - added new easyconfigs for existing toolchains: foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... @@ -71,6 +72,7 @@ feature + bugfix release - correct install location of OpenCV Python bindings (#3054) - include XZ as dependency for libunwind (#3055) - add patch to fix broken OpenSSL tests due to expired certificates (#3057) + - fix broken link to VSC website in license headers (#3062) v2.7.0 (March 20th 2016) -- GitLab From bc0544e7432494b9fd1d575f235fb60ecc473528 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 May 2016 19:26:21 +0200 Subject: [PATCH 0876/2403] fix typo --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 55f4ecd971..295e4c0820 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -40,7 +40,7 @@ feature + bugfix release - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) - various bug fixes, including: - fix perl extensions download urls (#2738) - - add Autconf as build dep for GCCcore (#2772) + - add Autoconf as build dep for GCCcore (#2772) - fix versions of extensions in Bioconductor 3.2 bundles (#2769) - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) - use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812) -- GitLab From 662760e1f21edfe0f85eed40012d1be3413580b2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 18 May 2016 16:18:09 +1200 Subject: [PATCH 0877/2403] New generic EasyConfig for Molpro-mpp-2015.1.3 --- ...Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb new file mode 100644 index 0000000000..119e4e7dfb --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -0,0 +1,21 @@ +name = 'Molpro' +versionprefix = 'mpp-' +version = '2015.1.3' +versionsuffix = '.linux_x86_64_openmp' + +homepage = 'https://www.molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URL available, requires registration to download +sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] + +precompiled_binaries = True + +# license file - uncomment if a licence file is supplied by your site and +# is valid for all users - the value of license_file may have to be changed +#import os +#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') + +moduleclass = 'chem' -- GitLab From d6e1b94b159fa6e0412e1c8d31f7d1254324e4b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 07:11:37 +0200 Subject: [PATCH 0878/2403] fix minor style issue in v2.8.0 release notes --- RELEASE_NOTES | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 295e4c0820..bcf497ffd9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -36,10 +36,10 @@ feature + bugfix release - enhance ORCA easyconfig for compatibility with SLURM (#1819) - enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764) - clean up binutils easyconfigs to use binutils easyblock (#3006) - - add include/GraphicsMagick to CPATH in GraphicsMagick easyconfigs (#3034) + - add include/GraphicsMagick to $CPATH in GraphicsMagick easyconfigs (#3034) - update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050) - various bug fixes, including: - - fix perl extensions download urls (#2738) + - fix Perl extensions download urls (#2738) - add Autoconf as build dep for GCCcore (#2772) - fix versions of extensions in Bioconductor 3.2 bundles (#2769) - fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874) @@ -48,14 +48,13 @@ feature + bugfix release - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816) - fix homepage and description in Pygments easyconfigs (#2822) - include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827) - - consistently use XORG_*_SOURCE constants (#2829, #2830) + - consistently use XORG_*_SOURCE constants (#2829, #2830, #2848) - update source URLs in ScientificPython easyconfig files (#2847) - - use XORG_LIB_SOURCE in libICE/libSM easyconfigs (#2848) - add checksums in SuiteSparse easyconfigs (#2849) - fix build deps for GObject-Introspection (#2852) - correctly specify Perl location in git easyconfig (#2866) - fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880) - - fix Perl dependency in worker, it required non-standard Perl modules (#2884) + - fix Perl dependency in worker easyconfig, it requires non-standard Perl modules (#2884) - add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887) - fix download URL for packmol (#2902) - drop usempi toolchain in numexpr easyconfigs, not needed (#2937) -- GitLab From 7bca09efb06814a305de6ff5b41c1fedfd89ff22 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:46:28 +0200 Subject: [PATCH 0879/2403] fixed patch --- .../r/RSEM/RSEM-1.2.30-foss-2016a.eb | 47 +- .../r/RSEM/RSEM-1.2.30_boost.patch | 23 - .../r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch | 162 ------- .../r/RSEM/RSEM-1.2.30_makefiles.patch | 59 +++ easybuild/easyconfigs/r/RSEM/sam/Makefile | 314 ------------- .../easyconfigs/r/RSEM/sam/Makefile.orig | 314 ------------- easybuild/easyconfigs/r/RSEM/sam/diff | 23 - easybuild/easyconfigs/r/RSEM/sam/hts/Makefile | 426 ------------------ .../easyconfigs/r/RSEM/sam/hts/Makefile.orig | 426 ------------------ easybuild/easyconfigs/r/RSEM/sam/hts/diff | 18 - 10 files changed, 69 insertions(+), 1743 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch delete mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/Makefile.orig delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/diff delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig delete mode 100644 easybuild/easyconfigs/r/RSEM/sam/hts/diff diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb index 0daeb572d1..9b54daaecd 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'RSEM' version = '1.2.30' @@ -11,47 +11,20 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/deweylab/RSEM/archive/'] sources = ['v%(version)s.tar.gz'] -#patches = ['RSEM-%(version)s_boost.patch'] +#patches = ['RSEM-%(version)s_zlib.patch'] +patches = ['RSEM-%(version)s_makefiles.patch'] -dependencies = [ - ('ncurses', '6.0'), -] +skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" -list_of_executables = [ - "rsem_perl_utils.pm", - "rsem-bam2readdepth", - "rsem-bam2wig", - "rsem-build-read-index", - "rsem-calculate-credibility-intervals", - "rsem-calculate-expression", - "rsem-control-fdr", - "rsem-extract-reference-transcripts", - "rsem-generate-data-matrix", - "rsem-generate-ngvector", - "rsem-gen-transcript-plots", - "rsem-get-unique", - "rsem-gff3-to-gtf", - "rsem-parse-alignments", - "rsem-plot-model", - "rsem-plot-transcript-wiggles", - "rsem-prepare-reference", - "rsem-preref", - "rsem-refseq-extract-primary-assembly", - "rsem-run-ebseq", - "rsem-run-em", - "rsem-run-gibbs", - "rsem-sam-validator", - "rsem-scan-for-paired-end-reads", - "rsem-simulate-reads", - "rsem-synthesis-reference-transcripts", - "rsem-tbam2gbam", +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), ] -files_to_copy = [(list_of_executables, "bin"), "WHAT_IS_NEW"] - sanity_check_paths = { - 'files': ['''"bin/%s" % x for x in list_of_executables'''], - 'dirs': [], + 'files': [], + 'dirs': ['bin/samtools-1.3'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch deleted file mode 100644 index 5782cb6a2d..0000000000 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_boost.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- samtools-1.3/Makefile.orig 2016-05-13 11:39:28.000000000 +0200 -+++ samtools-1.3/Makefile 2016-05-13 11:42:52.000000000 +0200 -@@ -21,9 +21,9 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - CPPFLAGS = --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - LDFLAGS = - LIBS = - -@@ -83,7 +83,7 @@ - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally - ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch deleted file mode 100644 index 206ac1fda2..0000000000 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_eb_provided_zlib.patch +++ /dev/null @@ -1,162 +0,0 @@ -#Use EB provided libz and use EB provided CXX and CXXFLAGS -# January 11, 2016 by B. Hajgato (Vrije Ubiversiteit Brussel) ---- Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ Makefile 2016-01-18 12:02:56.406105229 +0100 -@@ -1,6 +1,6 @@ --CC = g++ --CFLAGS = -Wall -c -I. --COFLAGS = -Wall -O3 -ffast-math -c -I. -+#CC = g++ -+#CFLAGS = -Wall -c -I. -+COFLAGS = ${CXXFLAGS} -Wall -c -I. - PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads - - .PHONY : all ebseq clean -@@ -8,6 +8,8 @@ - all : $(PROGRAMS) - - sam/libbam.a : -+ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/Makefile -+ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i sam/bcftools/Makefile - cd sam ; ${MAKE} all - - Transcript.h : utils.h -@@ -15,10 +17,10 @@ - Transcripts.h : utils.h my_assert.h Transcript.h - - rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp -- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts -+ $(CXX) -Wall ${CXXFLAGS} extractRef.cpp -o rsem-extract-reference-transcripts - - rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp -- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts -+ $(CXX) -Wall ${CXXFLAGS} synthesisRef.cpp -o rsem-synthesis-reference-transcripts - - BowtieRefSeqPolicy.h : RefSeqPolicy.h - -@@ -28,10 +30,10 @@ - - - rsem-preref : preRef.o -- $(CC) preRef.o -o rsem-preref -+ $(CXX) preRef.o -o rsem-preref - - preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp -- $(CC) $(COFLAGS) preRef.cpp -+ $(CXX) $(COFLAGS) preRef.cpp - - - SingleRead.h : Read.h -@@ -52,14 +54,14 @@ - - - rsem-parse-alignments : parseIt.o sam/libbam.a -- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread -+ $(CXX) -o rsem-parse-alignments parseIt.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread - - parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp -- $(CC) -Wall -O2 -c -I. parseIt.cpp -+ $(CXX) $(COFLAGS) parseIt.cpp - - - rsem-build-read-index : utils.h buildReadIndex.cpp -- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index -+ $(CXX) ${CXXFLAGS} buildReadIndex.cpp -o rsem-build-read-index - - - simul.h : boost/random.hpp -@@ -87,57 +89,57 @@ - WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h - - rsem-run-em : EM.o sam/libbam.a -- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread -+ $(CXX) -o rsem-run-em EM.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread - - EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp -- $(CC) $(COFLAGS) EM.cpp -+ $(CXX) $(COFLAGS) EM.cpp - - bc_aux.h : sam/bam.h - - BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h - - rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a -- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall tbam2gbam.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp -- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall bam2wig.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp -- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h -- $(CC) $(COFLAGS) wiggle.cpp -+ $(CXX) $(COFLAGS) wiggle.cpp - - rsem-simulate-reads : simulation.o -- $(CC) -o rsem-simulate-reads simulation.o -+ $(CXX) -o rsem-simulate-reads simulation.o - - simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp -- $(CC) $(COFLAGS) simulation.cpp -+ $(CXX) $(COFLAGS) simulation.cpp - - rsem-run-gibbs : Gibbs.o -- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread -+ $(CXX) -o rsem-run-gibbs Gibbs.o -lpthread - - #some header files are omitted - Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp -- $(CC) $(COFLAGS) Gibbs.cpp -+ $(CXX) $(COFLAGS) Gibbs.cpp - - Buffer.h : my_assert.h - - rsem-calculate-credibility-intervals : calcCI.o -- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread -+ $(CXX) -o rsem-calculate-credibility-intervals calcCI.o -lpthread - - #some header files are omitted - calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp -- $(CC) $(COFLAGS) calcCI.cpp -+ $(CXX) $(COFLAGS) calcCI.cpp - - rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a -- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall getUnique.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a -- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall samValidator.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a -- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ -+ $(CXX) ${CXXFLAGS} -Wall scanForPairedEndReads.cpp sam/libbam.a -L${EBROOTZLIB}/lib -lz -lpthread -o $@ - - ebseq : - cd EBSeq ; ${MAKE} all ---- sam/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ sam/Makefile 2016-01-18 12:08:43.769066188 +0100 -@@ -1,7 +1,7 @@ --CC= gcc -+#CC= gcc - CFLAGS_EXTRA= - #CFLAGS_EXTRA= -L/usr/include/ncurses --CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) -+#CFLAGS= -g -Wall -O2 $(CFLAGS_EXTRA) - #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib - DFLAGS_EXTRA= - #DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log ---- sam/bcftools/Makefile.orig 2016-01-08 02:23:01.000000000 +0100 -+++ sam/bcftools/Makefile 2016-01-18 12:09:10.076063429 +0100 -@@ -1,5 +1,5 @@ --CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc -+#CC= gcc -+#CFLAGS= -g -Wall -O2 #-m64 #-arch ppc - DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE - LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o - OMISC= .. \ No newline at end of file diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch new file mode 100644 index 0000000000..483f79b1f2 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch @@ -0,0 +1,59 @@ +--- RSEM-1.2.30/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/Makefile 2016-05-13 16:25:04.000000000 +0200 +@@ -11,12 +11,12 @@ + BOOST = . + + # Compilation variables +-CXX = g++ +-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +-CPPFLAGS = ++#CXX = g++ ++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++#CPPFLAGS = + +-LDFLAGS = +-LDLIBS = ++#LDFLAGS = ++#LDLIBS = + + # Installation variables + INSTALL = install +--- RSEM-1.2.30/samtools-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/Makefile 2016-05-13 16:25:42.000000000 +0200 +@@ -21,10 +21,10 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = +-CFLAGS = -g -Wall -O2 +-LDFLAGS = ++#CC = gcc ++#CPPFLAGS = ++#CFLAGS = -g -Wall -O2 ++#LDFLAGS = + LIBS = + + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +--- RSEM-1.2.30/samtools-1.3/htslib-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/htslib-1.3/Makefile 2016-05-13 16:26:24.000000000 +0200 +@@ -22,15 +22,15 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + AR = ar + RANLIB = ranlib + +-CPPFLAGS = ++#CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = ++#LDFLAGS = + LIBS = + + # For now these don't work too well as samtools also needs to know to diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile b/easybuild/easyconfigs/r/RSEM/sam/Makefile deleted file mode 100644 index c7e392d67c..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/Makefile +++ /dev/null @@ -1,314 +0,0 @@ -# Makefile for samtools, utilities for the Sequence Alignment/Map format. -# -# Copyright (C) 2008-2015 Genome Research Ltd. -# Portions copyright (C) 2010-2012 Broad Institute. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -#CC = gcc -CPPFLAGS = -#CFLAGS = -g -Wall -O2 -LDFLAGS = -LIBS = - -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -AOBJS= bam_index.o bam_plcmd.o sam_view.o \ - bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ - bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ - bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ - faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - - -PROGRAMS = samtools - -BUILT_MISC_PROGRAMS = \ - misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ - misc/md5fa misc/md5sum-lite misc/wgsim - -MISC_PROGRAMS = \ - $(BUILT_MISC_PROGRAMS) \ - misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ - misc/interpolate_sam.pl misc/novo2sam.pl \ - misc/plot-bamstats misc/psl2sam.pl \ - misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ - misc/soap2sam.pl \ - misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl - -BUILT_TEST_PROGRAMS = \ - test/merge/test_bam_translate \ - test/merge/test_rtrans_build \ - test/merge/test_trans_tbl_init \ - test/split/test_count_rg \ - test/split/test_expand_format_string \ - test/split/test_filter_header_rg \ - test/split/test_parse_args \ - test/vcf-miniview - -all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally -ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) -ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - -# Usually config.mk and config.h are generated by running configure -# or config.status, but if those aren't used create defaults here. - -config.mk: - @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ - -config.h: - echo '/* Basic config.h generated by Makefile */' > $@ - echo '#define HAVE_CURSES' >> $@ - echo '#define HAVE_CURSES_H' >> $@ - -include config.mk - - -PACKAGE_VERSION = 1.3 - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, -# comment out this conditional. -ifneq "$(wildcard .git)" "" -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -# If you don't have GNU Make but are building from a Git repository, you may -# wish to replace this with a rule that always rebuilds version.h: -# version.h: force -# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ -version.h: - echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .c .o - -.c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - - -lib:libbam.a - -libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - -samtools: $(AOBJS) libbam.a $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) - -bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) -bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h -bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) -bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) -bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) -sam_h = sam.h $(htslib_sam_h) $(bam_h) -sam_opts_h = sam_opts.h $(htslib_hts_h) -sample_h = sample.h $(htslib_kstring_h) - -bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h -bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h -bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) -bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) -bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -bam_aux.o: bam_aux.c $(bam_h) -bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) -bam_color.o: bam_color.c $(bam_h) -bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) -bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h -bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) -bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) -bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) -bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) -bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) -bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h -bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) -bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) -bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) -bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) -bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h -bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) -bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) -bam_tview_html.o: bam_tview_html.c $(bam_tview_h) -bam_flags.o: bam_flags.c $(htslib_sam_h) -bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) -bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h -bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) -bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) -cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) -dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) -errmod.o: errmod.c errmod.h $(htslib_ksort_h) -kprobaln.o: kprobaln.c kprobaln.h -padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) -phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) -sam.o: sam.c $(htslib_faidx_h) $(sam_h) -sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) -sam_opts.o: sam_opts.c $(sam_opts_h) -sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) -sample.o: sample.c $(sample_h) $(htslib_khash_h) -stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) -stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) - - -# test programs - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -# (regression.sh sets $REF_PATH to a subdirectory itself.) -check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_rtrans_build - test/merge/test_trans_tbl_init - cd test/mpileup && ./regression.sh mpileup.reg - cd test/mpileup && ./regression.sh depth.reg - test/split/test_count_rg - test/split/test_expand_format_string - test/split/test_filter_header_rg - test/split/test_parse_args - - -test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) - -test_test_h = test/test.h $(htslib_sam_h) - -test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) -test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o -test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o -test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) -test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) -test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) -test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) -test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) -test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) - - -# misc programs - -misc/ace2sam: misc/ace2sam.o - $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - -misc/maq2sam-short: misc/maq2sam-short.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - -misc/maq2sam-long: misc/maq2sam-long.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - -misc/md5fa: misc/md5fa.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - -misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) -misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) -misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) -misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) - -misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - -misc/maq2sam-long.o: misc/maq2sam.c - $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - - -install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) - - -testclean: - -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* - -cd test/dat && rm -f test_input_*.bam.bai - -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* - -mostlyclean: testclean - -rm -f *.o misc/*.o test/*.o test/*/*.o version.h - -clean: mostlyclean - -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -distclean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS - -clean-all: clean clean-htslib - - -tags: - ctags -f TAGS *.[ch] misc/*.[ch] - - -force: - - -.PHONY: all check clean clean-all distclean force install -.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig deleted file mode 100644 index 525288c2c8..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/Makefile.orig +++ /dev/null @@ -1,314 +0,0 @@ -# Makefile for samtools, utilities for the Sequence Alignment/Map format. -# -# Copyright (C) 2008-2015 Genome Research Ltd. -# Portions copyright (C) 2010-2012 Broad Institute. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -CC = gcc -CPPFLAGS = -CFLAGS = -g -Wall -O2 -LDFLAGS = -LIBS = - -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o -AOBJS= bam_index.o bam_plcmd.o sam_view.o \ - bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \ - bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ - bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o \ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ - faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - - -PROGRAMS = samtools - -BUILT_MISC_PROGRAMS = \ - misc/ace2sam misc/maq2sam-long misc/maq2sam-short \ - misc/md5fa misc/md5sum-lite misc/wgsim - -MISC_PROGRAMS = \ - $(BUILT_MISC_PROGRAMS) \ - misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ - misc/interpolate_sam.pl misc/novo2sam.pl \ - misc/plot-bamstats misc/psl2sam.pl \ - misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \ - misc/soap2sam.pl \ - misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl - -BUILT_TEST_PROGRAMS = \ - test/merge/test_bam_translate \ - test/merge/test_rtrans_build \ - test/merge/test_trans_tbl_init \ - test/split/test_count_rg \ - test/split/test_expand_format_string \ - test/split/test_filter_header_rg \ - test/split/test_parse_args \ - test/vcf-miniview - -all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally -ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) -ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -ldl $(LIBS) - -# Usually config.mk and config.h are generated by running configure -# or config.status, but if those aren't used create defaults here. - -config.mk: - @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.3#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ - -config.h: - echo '/* Basic config.h generated by Makefile */' > $@ - echo '#define HAVE_CURSES' >> $@ - echo '#define HAVE_CURSES_H' >> $@ - -include config.mk - - -PACKAGE_VERSION = 1.3 - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# $(shell), :=, etc are GNU Make-specific. If you don't have GNU Make, -# comment out this conditional. -ifneq "$(wildcard .git)" "" -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -# If you don't have GNU Make but are building from a Git repository, you may -# wish to replace this with a rule that always rebuilds version.h: -# version.h: force -# echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@ -version.h: - echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .c .o - -.c.o: - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< - - -lib:libbam.a - -libbam.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - -samtools: $(AOBJS) libbam.a $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) - -bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) -bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h -bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) -bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) -bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) -sam_h = sam.h $(htslib_sam_h) $(bam_h) -sam_opts_h = sam_opts.h $(htslib_hts_h) -sample_h = sample.h $(htslib_kstring_h) - -bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h -bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h -bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h) -bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h) -bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) -bam_aux.o: bam_aux.c $(bam_h) -bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) -bam_color.o: bam_color.c $(bam_h) -bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) -bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h -bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) -bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) -bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h) -bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) -bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) -bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h) -bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h -bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h) -bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) -bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) -bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h) -bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h -bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h) -bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) -bam_tview_html.o: bam_tview_html.c $(bam_tview_h) -bam_flags.o: bam_flags.c $(htslib_sam_h) -bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) -bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h -bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) -bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) -cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h) -dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h) -errmod.o: errmod.c errmod.h $(htslib_ksort_h) -kprobaln.o: kprobaln.c kprobaln.h -padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) -phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) -sam.o: sam.c $(htslib_faidx_h) $(sam_h) -sam_header.o: sam_header.c sam_header.h $(htslib_khash_h) -sam_opts.o: sam_opts.c $(sam_opts_h) -sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) -sample.o: sample.c $(sample_h) $(htslib_khash_h) -stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h) -stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) - - -# test programs - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -# (regression.sh sets $REF_PATH to a subdirectory itself.) -check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) - test/merge/test_bam_translate test/merge/test_bam_translate.tmp - test/merge/test_rtrans_build - test/merge/test_trans_tbl_init - cd test/mpileup && ./regression.sh mpileup.reg - cd test/mpileup && ./regression.sh depth.reg - test/split/test_count_rg - test/split/test_expand_format_string - test/split/test_filter_header_rg - test/split/test_parse_args - - -test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) - -test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) - $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) - -test_test_h = test/test.h $(htslib_sam_h) - -test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h) -test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o -test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o -test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h) -test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h) -test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h) -test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h) -test/test.o: test/test.c $(htslib_sam_h) $(test_test_h) -test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h) - - -# misc programs - -misc/ace2sam: misc/ace2sam.o - $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) - -misc/maq2sam-short: misc/maq2sam-short.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) - -misc/maq2sam-long: misc/maq2sam-long.o - $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) - -misc/md5fa: misc/md5fa.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) - $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) - -misc/wgsim: misc/wgsim.o - $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) - -misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h) -misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h) -misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h) -misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h) - -misc/maq2sam-short.o: misc/maq2sam.c - $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - -misc/maq2sam-long.o: misc/maq2sam.c - $(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c - - -install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) - - -testclean: - -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* - -cd test/dat && rm -f test_input_*.bam.bai - -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam* - -mostlyclean: testclean - -rm -f *.o misc/*.o test/*.o test/*/*.o version.h - -clean: mostlyclean - -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - -distclean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS - -clean-all: clean clean-htslib - - -tags: - ctags -f TAGS *.[ch] misc/*.[ch] - - -force: - - -.PHONY: all check clean clean-all distclean force install -.PHONY: lib mostlyclean print-version tags test testclean diff --git a/easybuild/easyconfigs/r/RSEM/sam/diff b/easybuild/easyconfigs/r/RSEM/sam/diff deleted file mode 100644 index 2469cafcc9..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/diff +++ /dev/null @@ -1,23 +0,0 @@ ---- Makefile.orig 2016-05-13 11:39:28.000000000 +0200 -+++ Makefile 2016-05-13 12:29:50.000000000 +0200 -@@ -21,9 +21,9 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - CPPFLAGS = --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - LDFLAGS = - LIBS = - -@@ -83,7 +83,7 @@ - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally - ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz -L${EBROOTZLIB}/lib -ldl $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile deleted file mode 100644 index 00c103599b..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile +++ /dev/null @@ -1,426 +0,0 @@ -# Makefile for htslib, a C library for high-throughput sequencing data formats. -# -# Copyright (C) 2013-2015 Genome Research Ltd. -# -# Author: John Marshall -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -#CC = gcc -AR = ar -RANLIB = ranlib - -CPPFLAGS = -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat -#CFLAGS = -g -Wall -O2 -EXTRA_CFLAGS_PIC = -fpic -LDFLAGS = -LIBS = - -# For now these don't work too well as samtools also needs to know to -# add -lbz2 and -llzma if linking against the static libhts.a library. -# TODO This needs configury and adding to htslib.pc.in. -# -# # Bzip2 support; optionally used by CRAM. -# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBBZ2)" "yes" -# CPPFLAGS += -DHAVE_LIBBZ2 -# LIBS += -lbz2 -# endif -# -# # Lzma support; optionally used by CRAM. -# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBLZMA)" "yes" -# CPPFLAGS += -DHAVE_LIBLZMA -# LIBS += -llzma -# endif - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -includedir = $(prefix)/include -libdir = $(exec_prefix)/lib -libexecdir = $(exec_prefix)/libexec -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 -man5dir = $(mandir)/man5 -pkgconfigdir= $(libdir)/pkgconfig - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - -# Set by config.mk if plugins are enabled -plugindir = - -BUILT_PROGRAMS = \ - bgzip \ - htsfile \ - tabix - -BUILT_TEST_PROGRAMS = \ - test/fieldarith \ - test/hfile \ - test/sam \ - test/test-regidx \ - test/test_view \ - test/test-vcf-api \ - test/test-vcf-sweep - -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) - -HTSPREFIX = -include htslib_vars.mk - - -PACKAGE_VERSION = 1.3 -LIBHTS_SOVERSION = 1 - - -# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string -# even if this is a dirty or untagged Git working tree. -NUMERIC_VERSION = $(PACKAGE_VERSION) - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# Much of this is also GNU Make-specific. If you don't have GNU Make and/or -# are not building from a Git repository, comment out this conditional. -ifneq "$(wildcard .git)" "" -original_version := $(PACKAGE_VERSION) -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag -# with a numeric name, revert $(NUMERIC_VERSION) to the original version number -# written above, but with the patchlevel field bumped to 255. -ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." -empty := -NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) -endif - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -version.h: - echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .bundle .c .o .pico .so - -.c.o: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< - -.c.pico: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< - - -LIBHTS_OBJS = \ - kfunc.o \ - knetfile.o \ - kstring.o \ - bgzf.o \ - faidx.o \ - hfile.o \ - hfile_net.o \ - hts.o \ - md5.o \ - regidx.o \ - sam.o \ - synced_bcf_reader.o \ - vcf_sweep.o \ - tbx.o \ - vcf.o \ - vcfutils.o \ - cram/cram_codecs.o \ - cram/cram_decode.o \ - cram/cram_encode.o \ - cram/cram_external.o \ - cram/cram_index.o \ - cram/cram_io.o \ - cram/cram_samtools.o \ - cram/cram_stats.o \ - cram/files.o \ - cram/mFILE.o \ - cram/open_trace_file.o \ - cram/pooled_alloc.o \ - cram/rANS_static.o \ - cram/sam_header.o \ - cram/string_alloc.o \ - cram/thread_pool.o \ - cram/vlen.o \ - cram/zfio.o - -PLUGIN_OBJS = - -cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) -cram_io_h = cram/cram_io.h $(cram_misc_h) -cram_misc_h = cram/misc.h cram/os.h -cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) -cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) -cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) -cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h -hfile_internal_h = hfile_internal.h $(htslib_hfile_h) -hts_internal_h = hts_internal.h $(htslib_hts_h) - - -# To be effective, config.mk needs to appear after most Makefile variables are -# set but before most rules appear, so that it can both use previously-set -# variables in its own rules' prerequisites and also update variables for use -# in later rules' prerequisites. - -# If your make doesn't accept -include, change this to 'include' if you are -# using the configure script or just comment the line out if you are not. --include config.mk - -# Usually config.h is generated by running configure or config.status, -# but if those aren't used create a default config.h here. -config.h: - echo '/* Empty config.h generated by Makefile */' > $@ - - -lib-static: libhts.a - -# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have -# GNU Make, comment out the parts of this conditional that don't apply. -PLATFORM := $(shell uname -s) -ifeq "$(PLATFORM)" "Darwin" -SHLIB_FLAVOUR = dylib -lib-shared: libhts.dylib -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) -else -SHLIB_FLAVOUR = so -lib-shared: libhts.so -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) -endif - -plugins: $(BUILT_PLUGINS) - - -libhts.a: $(LIBHTS_OBJS) - @-rm -f $@ - $(AR) -rc $@ $(LIBHTS_OBJS) - -$(RANLIB) $@ - - -# The target here is libhts.so, as that is the built file that other rules -# depend upon and that is used when -lhts appears in other program's recipes. -# As a byproduct invisible to make, libhts.so.NN is also created, as it is the -# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). - -libhts.so: $(LIBHTS_OBJS:.o=.pico) - $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) - ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) - -# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs -# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH -# includes this project's build directory). - -libhts.dylib: $(LIBHTS_OBJS) - $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) - ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib - - -.pico.so: - $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) - -.o.bundle: - $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) - - -bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) -kstring.o kstring.pico: kstring.c $(htslib_kstring_h) -knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) -hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) -hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) -hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) -vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) -sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) -tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) -faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) -synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) -vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) -vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) -kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) -regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) -md5.o md5.pico: md5.c config.h $(htslib_hts_h) -plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) - -cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) -cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) -cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) -cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) -cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) -cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h -cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) -cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h -cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) -cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h -cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h -cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h -cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h -cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h -cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h -cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h - - -bgzip: bgzip.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) - -htsfile: htsfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) - -tabix: tabix.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) - -bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) -htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) -tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) - - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -check test: htsfile $(BUILT_TEST_PROGRAMS) - test/fieldarith test/fieldarith.sam - test/hfile - test/sam test/ce.fa test/faidx.fa - test/test-regidx - cd test && REF_PATH=: ./test_view.pl - cd test && REF_PATH=: ./test.pl - -test/fieldarith: test/fieldarith.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) - -test/hfile: test/hfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) - -test/sam: test/sam.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) - -test/test-regidx: test/test-regidx.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) - -test/test_view: test/test_view.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) - -test/test-vcf-api: test/test-vcf-api.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) - -test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) - -test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) -test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) -test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) -test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) -test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) -test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) -test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) - - -install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig - $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) - if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi - $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib - $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a - $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) - $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) - -installdirs: - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) - if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi - -# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, -# with symlinks libhts.so (used via -lhts during linking of client programs) -# and libhts.so.NN (used by client executables at runtime). - -install-so: libhts.so installdirs - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) - -install-dylib: libhts.dylib installdirs - $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib - -# Substitute these pseudo-autoconf variables only at install time -# so that "make install prefix=/prefix/path" etc continue to work. -install-pkgconfig: installdirs - sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc - chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc - -# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides -# flags for building against the uninstalled library in this build directory. -htslib-uninstalled.pc: htslib.pc.in - sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ - - -testclean: - -rm -f test/*.tmp test/*.tmp.* - -mostlyclean: testclean - -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h - -clean: mostlyclean clean-$(SHLIB_FLAVOUR) - -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) - -distclean maintainer-clean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS *-uninstalled.pc - -clean-so: - -rm -f libhts.so libhts.so.* - -clean-dylib: - -rm -f libhts.dylib libhts.*.dylib - - -tags TAGS: - ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h - -# We recommend libhts-using programs be built against a separate htslib -# installation. However if you feel that you must bundle htslib source -# code with your program, this hook enables Automake-style "make dist" -# for this subdirectory. If you do bundle an htslib snapshot, please -# add identifying information to $(PACKAGE_VERSION) as appropriate. -# (The wildcards attempt to omit non-exported files (.git*, README.md, -# etc) and other detritus that might be in the top-level directory.) -distdir: - tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) - +cd $(distdir) && $(MAKE) distclean - -force: - - -.PHONY: all check clean distclean distdir force -.PHONY: install install-pkgconfig installdirs lib-shared lib-static -.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean -.PHONY: clean-so install-so -.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig b/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig deleted file mode 100644 index be2405e71c..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/Makefile.orig +++ /dev/null @@ -1,426 +0,0 @@ -# Makefile for htslib, a C library for high-throughput sequencing data formats. -# -# Copyright (C) 2013-2015 Genome Research Ltd. -# -# Author: John Marshall -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL -# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -# DEALINGS IN THE SOFTWARE. - -CC = gcc -AR = ar -RANLIB = ranlib - -CPPFLAGS = -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat -CFLAGS = -g -Wall -O2 -EXTRA_CFLAGS_PIC = -fpic -LDFLAGS = -LIBS = - -# For now these don't work too well as samtools also needs to know to -# add -lbz2 and -llzma if linking against the static libhts.a library. -# TODO This needs configury and adding to htslib.pc.in. -# -# # Bzip2 support; optionally used by CRAM. -# HAVE_LIBBZ2 := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBBZ2)" "yes" -# CPPFLAGS += -DHAVE_LIBBZ2 -# LIBS += -lbz2 -# endif -# -# # Lzma support; optionally used by CRAM. -# HAVE_LIBLZMA := $(shell echo -e "\#include \012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) -# ifeq "$(HAVE_LIBLZMA)" "yes" -# CPPFLAGS += -DHAVE_LIBLZMA -# LIBS += -llzma -# endif - -prefix = /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin -includedir = $(prefix)/include -libdir = $(exec_prefix)/lib -libexecdir = $(exec_prefix)/libexec -datarootdir = $(prefix)/share -mandir = $(datarootdir)/man -man1dir = $(mandir)/man1 -man5dir = $(mandir)/man5 -pkgconfigdir= $(libdir)/pkgconfig - -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 - -# Set by config.mk if plugins are enabled -plugindir = - -BUILT_PROGRAMS = \ - bgzip \ - htsfile \ - tabix - -BUILT_TEST_PROGRAMS = \ - test/fieldarith \ - test/hfile \ - test/sam \ - test/test-regidx \ - test/test_view \ - test/test-vcf-api \ - test/test-vcf-sweep - -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) - -HTSPREFIX = -include htslib_vars.mk - - -PACKAGE_VERSION = 1.3 -LIBHTS_SOVERSION = 1 - - -# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string -# even if this is a dirty or untagged Git working tree. -NUMERIC_VERSION = $(PACKAGE_VERSION) - -# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git -# description of the working tree: either a release tag with the same value -# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag. -# Much of this is also GNU Make-specific. If you don't have GNU Make and/or -# are not building from a Git repository, comment out this conditional. -ifneq "$(wildcard .git)" "" -original_version := $(PACKAGE_VERSION) -PACKAGE_VERSION := $(shell git describe --always --dirty) - -# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag -# with a numeric name, revert $(NUMERIC_VERSION) to the original version number -# written above, but with the patchlevel field bumped to 255. -ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "." -empty := -NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255) -endif - -# Force version.h to be remade if $(PACKAGE_VERSION) has changed. -version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force)) -endif - -version.h: - echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@ - -print-version: - @echo $(PACKAGE_VERSION) - - -.SUFFIXES: .bundle .c .o .pico .so - -.c.o: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $< - -.c.pico: - $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< - - -LIBHTS_OBJS = \ - kfunc.o \ - knetfile.o \ - kstring.o \ - bgzf.o \ - faidx.o \ - hfile.o \ - hfile_net.o \ - hts.o \ - md5.o \ - regidx.o \ - sam.o \ - synced_bcf_reader.o \ - vcf_sweep.o \ - tbx.o \ - vcf.o \ - vcfutils.o \ - cram/cram_codecs.o \ - cram/cram_decode.o \ - cram/cram_encode.o \ - cram/cram_external.o \ - cram/cram_index.o \ - cram/cram_io.o \ - cram/cram_samtools.o \ - cram/cram_stats.o \ - cram/files.o \ - cram/mFILE.o \ - cram/open_trace_file.o \ - cram/pooled_alloc.o \ - cram/rANS_static.o \ - cram/sam_header.o \ - cram/string_alloc.o \ - cram/thread_pool.o \ - cram/vlen.o \ - cram/zfio.o - -PLUGIN_OBJS = - -cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h) -cram_io_h = cram/cram_io.h $(cram_misc_h) -cram_misc_h = cram/misc.h cram/os.h -cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) -cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h) -cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h) -cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h -hfile_internal_h = hfile_internal.h $(htslib_hfile_h) -hts_internal_h = hts_internal.h $(htslib_hts_h) - - -# To be effective, config.mk needs to appear after most Makefile variables are -# set but before most rules appear, so that it can both use previously-set -# variables in its own rules' prerequisites and also update variables for use -# in later rules' prerequisites. - -# If your make doesn't accept -include, change this to 'include' if you are -# using the configure script or just comment the line out if you are not. --include config.mk - -# Usually config.h is generated by running configure or config.status, -# but if those aren't used create a default config.h here. -config.h: - echo '/* Empty config.h generated by Makefile */' > $@ - - -lib-static: libhts.a - -# $(shell), :=, and ifeq/.../endif are GNU Make-specific. If you don't have -# GNU Make, comment out the parts of this conditional that don't apply. -PLATFORM := $(shell uname -s) -ifeq "$(PLATFORM)" "Darwin" -SHLIB_FLAVOUR = dylib -lib-shared: libhts.dylib -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle) -else -SHLIB_FLAVOUR = so -lib-shared: libhts.so -BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so) -endif - -plugins: $(BUILT_PLUGINS) - - -libhts.a: $(LIBHTS_OBJS) - @-rm -f $@ - $(AR) -rc $@ $(LIBHTS_OBJS) - -$(RANLIB) $@ - - -# The target here is libhts.so, as that is the built file that other rules -# depend upon and that is used when -lhts appears in other program's recipes. -# As a byproduct invisible to make, libhts.so.NN is also created, as it is the -# file used at runtime (when $LD_LIBRARY_PATH includes the build directory). - -libhts.so: $(LIBHTS_OBJS:.o=.pico) - $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) - ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) - -# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs -# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH -# includes this project's build directory). - -libhts.dylib: $(LIBHTS_OBJS) - $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS) - ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib - - -.pico.so: - $(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS) - -.o.bundle: - $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS) - - -bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h) -kstring.o kstring.pico: kstring.c $(htslib_kstring_h) -knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h) -hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h) -hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) -hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h) -hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h) -vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) -sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) -tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h) -faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) -synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) -vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h) -vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h) -kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h) -regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) -md5.o md5.pico: md5.c config.h $(htslib_hts_h) -plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h) - -cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h) -cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h) -cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h) -cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h) -cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) -cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h) -cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h -cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h) -cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h -cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) -cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h -cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h -cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h -cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h -cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h -cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h -cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h - - -bgzip: bgzip.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS) - -htsfile: htsfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS) - -tabix: tabix.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS) - -bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) -htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h) -tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) - - -# For tests that might use it, set $REF_PATH explicitly to use only reference -# areas within the test suite (or set it to ':' to use no reference areas). -check test: htsfile $(BUILT_TEST_PROGRAMS) - test/fieldarith test/fieldarith.sam - test/hfile - test/sam test/ce.fa test/faidx.fa - test/test-regidx - cd test && REF_PATH=: ./test_view.pl - cd test && REF_PATH=: ./test.pl - -test/fieldarith: test/fieldarith.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS) - -test/hfile: test/hfile.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS) - -test/sam: test/sam.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS) - -test/test-regidx: test/test-regidx.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS) - -test/test_view: test/test_view.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS) - -test/test-vcf-api: test/test-vcf-api.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS) - -test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a - $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS) - -test/fieldarith.o: test/fieldarith.c $(htslib_sam_h) -test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h) -test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) -test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h) -test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h) -test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h) -test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h) - - -install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig - $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir) - if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi - $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib - $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a - $(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir) - $(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir) - -installdirs: - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir) - if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi - -# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z, -# with symlinks libhts.so (used via -lhts during linking of client programs) -# and libhts.so.NN (used by client executables at runtime). - -install-so: libhts.so installdirs - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so - ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) - -install-dylib: libhts.dylib installdirs - $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib - ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib - -# Substitute these pseudo-autoconf variables only at install time -# so that "make install prefix=/prefix/path" etc continue to work. -install-pkgconfig: installdirs - sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc - chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc - -# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides -# flags for building against the uninstalled library in this build directory. -htslib-uninstalled.pc: htslib.pc.in - sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@ - - -testclean: - -rm -f test/*.tmp test/*.tmp.* - -mostlyclean: testclean - -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h - -clean: mostlyclean clean-$(SHLIB_FLAVOUR) - -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) - -distclean maintainer-clean: clean - -rm -f config.cache config.h config.log config.mk config.status - -rm -f TAGS *-uninstalled.pc - -clean-so: - -rm -f libhts.so libhts.so.* - -clean-dylib: - -rm -f libhts.dylib libhts.*.dylib - - -tags TAGS: - ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h - -# We recommend libhts-using programs be built against a separate htslib -# installation. However if you feel that you must bundle htslib source -# code with your program, this hook enables Automake-style "make dist" -# for this subdirectory. If you do bundle an htslib snapshot, please -# add identifying information to $(PACKAGE_VERSION) as appropriate. -# (The wildcards attempt to omit non-exported files (.git*, README.md, -# etc) and other detritus that might be in the top-level directory.) -distdir: - tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x) - +cd $(distdir) && $(MAKE) distclean - -force: - - -.PHONY: all check clean distclean distdir force -.PHONY: install install-pkgconfig installdirs lib-shared lib-static -.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean -.PHONY: clean-so install-so -.PHONY: clean-dylib install-dylib diff --git a/easybuild/easyconfigs/r/RSEM/sam/hts/diff b/easybuild/easyconfigs/r/RSEM/sam/hts/diff deleted file mode 100644 index 97af9b3e44..0000000000 --- a/easybuild/easyconfigs/r/RSEM/sam/hts/diff +++ /dev/null @@ -1,18 +0,0 @@ ---- Makefile.orig 2016-05-13 12:08:45.000000000 +0200 -+++ Makefile 2016-05-13 12:10:21.000000000 +0200 -@@ -22,13 +22,13 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+#CC = gcc - AR = ar - RANLIB = ranlib - - CPPFLAGS = - # TODO: probably update cram code to make it compile cleanly with -Wc++-compat --CFLAGS = -g -Wall -O2 -+#CFLAGS = -g -Wall -O2 - EXTRA_CFLAGS_PIC = -fpic - LDFLAGS = - LIBS = -- GitLab From 0254d8662fae60a862eafae16a99fa71776a81b2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:50:12 +0200 Subject: [PATCH 0880/2403] provided author and reason for patch --- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch index 483f79b1f2..4edfe60165 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30_makefiles.patch @@ -1,3 +1,5 @@ +# Remove preset CXX and CPPFLAGS for each makefile, such that it uses the ones defined by EB. +# Author: Bob Dröge - Rijksuniversiteit Groningen (RUG) --- RSEM-1.2.30/Makefile 2016-04-20 23:59:26.000000000 +0200 +++ RSEM-1.2.30.new/Makefile 2016-05-13 16:25:04.000000000 +0200 @@ -11,12 +11,12 @@ -- GitLab From 210ea5bae0fc66c42acbabfb2a162ca3e52fbb40 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 09:53:02 +0200 Subject: [PATCH 0881/2403] removed files --- easybuild/easyconfigs/r/RSEM/Makefile | 173 --------------------- easybuild/easyconfigs/r/RSEM/Makefile.orig | 173 --------------------- 2 files changed, 346 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RSEM/Makefile delete mode 100644 easybuild/easyconfigs/r/RSEM/Makefile.orig diff --git a/easybuild/easyconfigs/r/RSEM/Makefile b/easybuild/easyconfigs/r/RSEM/Makefile deleted file mode 100644 index 921b40b1b3..0000000000 --- a/easybuild/easyconfigs/r/RSEM/Makefile +++ /dev/null @@ -1,173 +0,0 @@ -SAMTOOLS = samtools-1.3 -HTSLIB = htslib-1.3 - -ifneq ($(cygwin), true) - SAMTOOLS_MAKEFILE = Makefile -else - SAMTOOLS_MAKEFILE = Makefile.cygwin -endif - -# overridable, defaulting to local copy -BOOST = ${EBROOTBOOST} - -# Compilation variables -CXX = g++ -CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) -CPPFLAGS = - -LDFLAGS = -LDLIBS = - -# Installation variables -INSTALL = install -INSTALL_PROGRAM = $(INSTALL) -p -INSTALL_DATA = $(INSTALL) -p -m 644 -INSTALL_DIR = $(INSTALL) -d -STRIP ?=strip - -prefix ?= /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin - -# Auxiliary variables for compilation -SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h -SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a -CONFIGURE = ./configure - -OBJS1 = parseIt.o -OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o -OBJS3 = EM.o Gibbs.o calcCI.o simulation.o - -PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads -PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads -PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals - -PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) - -# Auxiliary variables for installation -SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ - rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ - extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem - - - - -.PHONY : all ebseq clean - -all : $(PROGRAMS) $(SAMTOOLS)/samtools - -$(SAMTOOLS)/samtools : - cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools - -$(SAMLIBS) : $(SAMTOOLS)/samtools - - -# Compile objects -$(OBJS1) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< - -$(OBJS2) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< - -$(OBJS3) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< - - -# Generate executables -$(PROGS1) : - $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) - -$(PROGS2) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -L$(EBROOTZLIB)/lib -lz - -$(PROGS3) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) - - -# Dependencies for executables -rsem-extract-reference-transcripts : extractRef.o -rsem-synthesis-reference-transcripts : synthesisRef.o -rsem-preref : preRef.o -rsem-build-read-index : buildReadIndex.o -rsem-simulate-reads : simulation.o - -rsem-parse-alignments : parseIt.o $(SAMLIBS) -rsem-run-em : EM.o SamHeader.o $(SAMLIBS) -rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) -rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) -rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) -rsem-get-unique : getUnique.o $(SAMLIBS) -rsem-sam-validator : samValidator.o $(SAMLIBS) -rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) - -rsem-run-gibbs : Gibbs.o -rsem-calculate-credibility-intervals : calcCI.o $(LDLIBS) - -# Dependencies for objects -parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h - -extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h -synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h -preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h -buildReadIndex.o : buildReadIndex.cpp utils.h -wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h -tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h -bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h -bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h -getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h -samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp - -EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h -Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h -calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h -simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h - -# Dependencies for header files -Transcript.h : utils.h -Transcripts.h : utils.h my_assert.h Transcript.h -BowtieRefSeqPolicy.h : RefSeqPolicy.h -RefSeq.h : utils.h -Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h -SingleRead.h : Read.h -SingleReadQ.h : Read.h -PairedEndRead.h : Read.h SingleRead.h -PairedEndReadQ.h : Read.h SingleReadQ.h -PairedEndHit.h : SingleHit.h -HitContainer.h : GroupInfo.h -sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h -SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h -simul.h : $(BOOST)/boost/random.hpp -ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h -SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h -SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h -PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h -PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h -HitWrapper.h : HitContainer.h -BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h -sampling.h : $(BOOST)/boost/random.hpp -WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h -bc_aux.h : $(SAMHEADERS) -BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h -Buffer.h : my_assert.h -SamHeader.hpp : $(SAMHEADERS) - -# Compile EBSeq -ebseq : - cd EBSeq && $(MAKE) all - -# Install RSEM -install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) - $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) - $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) - $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm - -# Clean -clean : - rm -f *.o *~ $(PROGRAMS) - cd $(SAMTOOLS) && $(MAKE) clean-all - cd EBSeq && $(MAKE) clean diff --git a/easybuild/easyconfigs/r/RSEM/Makefile.orig b/easybuild/easyconfigs/r/RSEM/Makefile.orig deleted file mode 100644 index 09d2223b23..0000000000 --- a/easybuild/easyconfigs/r/RSEM/Makefile.orig +++ /dev/null @@ -1,173 +0,0 @@ -SAMTOOLS = samtools-1.3 -HTSLIB = htslib-1.3 - -ifneq ($(cygwin), true) - SAMTOOLS_MAKEFILE = Makefile -else - SAMTOOLS_MAKEFILE = Makefile.cygwin -endif - -# overridable, defaulting to local copy -BOOST = . - -# Compilation variables -CXX = g++ -CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) -CPPFLAGS = - -LDFLAGS = -LDLIBS = - -# Installation variables -INSTALL = install -INSTALL_PROGRAM = $(INSTALL) -p -INSTALL_DATA = $(INSTALL) -p -m 644 -INSTALL_DIR = $(INSTALL) -d -STRIP ?=strip - -prefix ?= /usr/local -exec_prefix = $(prefix) -bindir = $(exec_prefix)/bin - -# Auxiliary variables for compilation -SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h -SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a -CONFIGURE = ./configure - -OBJS1 = parseIt.o -OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o -OBJS3 = EM.o Gibbs.o calcCI.o simulation.o - -PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads -PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads -PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals - -PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3) - -# Auxiliary variables for installation -SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \ - rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \ - extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem - - - - -.PHONY : all ebseq clean - -all : $(PROGRAMS) $(SAMTOOLS)/samtools - -$(SAMTOOLS)/samtools : - cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools - -$(SAMLIBS) : $(SAMTOOLS)/samtools - - -# Compile objects -$(OBJS1) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $< - -$(OBJS2) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $< - -$(OBJS3) : - $(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $< - - -# Generate executables -$(PROGS1) : - $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) - -$(PROGS2) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz - -$(PROGS3) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) - - -# Dependencies for executables -rsem-extract-reference-transcripts : extractRef.o -rsem-synthesis-reference-transcripts : synthesisRef.o -rsem-preref : preRef.o -rsem-build-read-index : buildReadIndex.o -rsem-simulate-reads : simulation.o - -rsem-parse-alignments : parseIt.o $(SAMLIBS) -rsem-run-em : EM.o SamHeader.o $(SAMLIBS) -rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS) -rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS) -rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS) -rsem-get-unique : getUnique.o $(SAMLIBS) -rsem-sam-validator : samValidator.o $(SAMLIBS) -rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS) - -rsem-run-gibbs : Gibbs.o -rsem-calculate-credibility-intervals : calcCI.o - -# Dependencies for objects -parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h - -extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h -synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h -preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h -buildReadIndex.o : buildReadIndex.cpp utils.h -wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h -tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h -bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h -bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h -getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h -samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h -SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp - -EM.o : EM.cpp $(SAMHEADERS) utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h -Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h -calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h -simulation.o : simulation.cpp utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/boost/random.hpp WriteResults.h - -# Dependencies for header files -Transcript.h : utils.h -Transcripts.h : utils.h my_assert.h Transcript.h -BowtieRefSeqPolicy.h : RefSeqPolicy.h -RefSeq.h : utils.h -Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h -SingleRead.h : Read.h -SingleReadQ.h : Read.h -PairedEndRead.h : Read.h SingleRead.h -PairedEndReadQ.h : Read.h SingleReadQ.h -PairedEndHit.h : SingleHit.h -HitContainer.h : GroupInfo.h -sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h -SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h -simul.h : $(BOOST)/boost/random.hpp -ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h -SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h -SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h -PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h -PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h -HitWrapper.h : HitContainer.h -BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h -sampling.h : $(BOOST)/boost/random.hpp -WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h -bc_aux.h : $(SAMHEADERS) -BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h -Buffer.h : my_assert.h -SamHeader.hpp : $(SAMHEADERS) - -# Compile EBSeq -ebseq : - cd EBSeq && $(MAKE) all - -# Install RSEM -install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) - $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) - $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) - $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm - -# Clean -clean : - rm -f *.o *~ $(PROGRAMS) - cd $(SAMTOOLS) && $(MAKE) clean-all - cd EBSeq && $(MAKE) clean -- GitLab From 28666985979b191e3f3ff9c374b7beffa4298a8b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 18 May 2016 15:15:01 +0200 Subject: [PATCH 0882/2403] FIAT with foss 2016a --- .../FIAT-1.6.0-foss-2016a-Python-2.7.11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b24555e505 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order + instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating + arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('sympy', '1.0', '-Python-%(pyver)s'), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From bf0d2b35fc9b19bb7e5a1d5ebb4445685ef1e995 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 16:15:03 +0200 Subject: [PATCH 0883/2403] bump version to 2.9.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 64865babea..c52c2d0550 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.8.0' +VERSION = '2.9.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c65b54690235513636e7619ce7fdab3bbfaf0bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 May 2016 16:31:32 +0200 Subject: [PATCH 0884/2403] add easyconfig EasyBuild-2.8.0.eb --- .../e/EasyBuild/EasyBuild-2.8.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb new file mode 100644 index 0000000000..07bb77b453 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/1d/9e/9a69f54d7bdb4a75e78530d1ccdd66be5fd61e31ef289f167cf007e11089/', + 'https://pypi.python.org/packages/e9/c2/db36d5a92ddcb68645a64f9017a7056438aa40f224e09c3b6af374d58ebc/', + 'https://pypi.python.org/packages/c0/84/ebe0a2fc169370db663d82caf7c0224771028c79ec9a324b46d029840773/', + 'https://pypi.python.org/packages/ea/f2/a5556cc4e7f3dd4059d890b56a6af9ca80e9210993db65303aa0163806fd/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.4.18.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 81b7afc53a7220ab3196dd67f2ba2f81ec523bf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 10:38:38 +0200 Subject: [PATCH 0885/2403] add easyconfig Spark-1.6.1.eb --- easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb | 28 ++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb new file mode 100644 index 0000000000..e06636922a --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.6.1' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +checksums = ['667a62d7f289479a19da4b563e7151d4'] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 0e676c7588bcafcb57506cb3d124cf8dc67d076c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 10:47:51 +0200 Subject: [PATCH 0886/2403] fix source for snappy 1.1.3, drop autogen --- .../s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb | 21 +++++++++++++++++++ .../s/snappy/snappy-1.1.3-GCC-4.9.3.eb | 13 +++--------- 2 files changed, 24 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..25d6fcc3ba --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.3' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = ['https://github.com/google/snappy/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libsnappy.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb index 36e8b8b902..5e495e1a26 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb @@ -3,22 +3,15 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.3' -# snappy was migrated from code.google.com to github.com and this commit -# corresponds to release 1.1.2 (which they haven't tagged). -# see https://github.com/google/snappy/commit/1ff9be9 -commit = '1ff9be9' - -homepage = 'http://code.google.com/p/snappy/' +homepage = 'https://github.com/google/snappy' description = """Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.""" toolchain = {'name': 'GCC', 'version': '4.9.3'} -source_urls = ['https://github.com/google/snappy/archive'] -sources = ['%s.tar.gz' % commit] - -preconfigopts = "./autogen.sh && " +source_urls = ['https://github.com/google/snappy/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] sanity_check_paths = { 'files': ['lib/libsnappy.%s' % SHLIB_EXT], -- GitLab From 99f8995aa638826460dfb681ace651616c63f94b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:03:34 +0200 Subject: [PATCH 0887/2403] add testpath as dependency of IPython, rather than as extension --- ...IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 17 ++++------- .../pip-8.1.2-intel-2015a-Python-2.7.10.eb | 19 ++++++++++++ .../testpath-0.2-intel-2015a-Python-2.7.10.eb | 30 +++++++++++++++++++ 3 files changed, 54 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index aee1a02648..eacf19ae8d 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -2,6 +2,7 @@ easyblock = 'Bundle' name = 'IPython' version = '4.0.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -13,13 +14,9 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} -python = 'Python' -pyver = '2.7.10' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), + ('Python', '2.7.10'), + ('testpath', '0.2', versionsuffix), ] # this is a bundle of Python packages @@ -50,24 +47,20 @@ exts_list = [ ('requests', '2.7.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), - ('testpath', '0.2', { - 'source_urls': ['https://github.com/jupyter/testpath/archive/'], - 'source_tmpl': '%(version)s.tar.gz', - }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f8c928ec85 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.10'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..90a7f21775 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.10'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' -- GitLab From cd1f133df5a9a18ea5fe4c81d982725dde5da050 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:09:19 +0200 Subject: [PATCH 0888/2403] revert back to libreadline 6.3 in SQLite easyconfig --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 7b7e716a53..6a41f5863c 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -26,7 +26,7 @@ version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.spl sources = ['sqlite-autoconf-%s.tar.gz' % version_str] dependencies = [ - ('libreadline', '6.2'), + ('libreadline', '6.3'), ('Tcl', '8.6.4'), ] -- GitLab From dcd8260522e4ed83259fcf39bdd52f0986d3c6e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:28:07 +0200 Subject: [PATCH 0889/2403] downgrade to SQLite to fix libreadline conflict --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb | 37 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index af763e233d..fcbae3463e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -25,7 +25,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), - ('SQLite', '3.8.10.2'), + ('SQLite', '3.8.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ] diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..6f7046c321 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.5' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c4880662bf3b1931681e4aaf13e7ed33b1d15e79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 11:31:17 +0200 Subject: [PATCH 0890/2403] fix modulenam for path.py extension --- .../i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb index eacf19ae8d..4ba4b8c0f8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.0.0-intel-2015a-Python-2.7.10.eb @@ -36,6 +36,7 @@ exts_list = [ }), ('path.py', '7.6', { 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', }), ('pickleshare', '0.5', { 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], -- GitLab From 7b0872b489226825cb57886dce2cfa89bdc40fba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:20:22 +0200 Subject: [PATCH 0891/2403] add testpath as a dependency to IPython --- ...IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 9 ++---- .../pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb | 19 ++++++++++++ .../testpath-0.3-goolf-1.4.10-Python-2.7.5.eb | 30 +++++++++++++++++++ 3 files changed, 52 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index fcbae3463e..614af5bd06 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -27,6 +27,7 @@ dependencies = [ (python, pyver), ('SQLite', '3.8.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('testpath', '0.3', versionsuffix), ] # this is a bundle of Python packages @@ -131,10 +132,6 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), - #('testpath', '0.3', { - #'source_urls': ['https://github.com/jupyter/testpath/archive/'], #this extension doesn't provide a setup.py and it's required for the sanity checks (iptest, iptest2) - #'source_tmpl': '0.3.tar.gz', - #}), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', @@ -151,8 +148,8 @@ sanity_check_paths = { sanity_check_commands = [ ('ipython -h', ''), ('ipython notebook --help', ''), - #('iptest', ''), # this test fails with 'ImportError: No module named testpath'. testpath cannot be installed with easyconfig - #('iptest2', ''), + ('iptest', ''), + ('iptest2', ''), ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..79cbce5e37 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.5'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..8d9a62a9e3 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.5'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' -- GitLab From c3d233d23d2151c9c98a341051b666b239af129d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:22:20 +0200 Subject: [PATCH 0892/2403] add easyconfig netCDF-Fortran-4.4.4-intel-2016a.eb, add easyconfig netCDF-C++4-4.3.0-intel-2016a.eb --- .../netCDF-C++4-4.3.0-intel-2016a.eb | 24 +++++++++++++++++++ .../netCDF-Fortran-4.4.4-intel-2016a.eb | 17 +++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb new file mode 100644 index 0000000000..3243613e15 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb new file mode 100644 index 0000000000..947f018cb3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' -- GitLab From 912898e31a7dc99effb7c7fc9610b9a497354cf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 12:24:58 +0200 Subject: [PATCH 0893/2403] fix source URL for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb index 6f7046c321..72f8da9d34 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb @@ -18,8 +18,7 @@ version = '3.8.5' homepage = 'http://www.hwaci.com/sw/sqlite/' description = "SQLite: SQL Database Engine in a C Library" -# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +source_urls = ['http://www.sqlite.org/2014'] sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 389d679cd6e983b0025c75444b23641daa4835f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:03:04 +0200 Subject: [PATCH 0894/2403] add missing extension pexpect --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 614af5bd06..deb444d50b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -132,6 +132,9 @@ exts_list = [ ('ipykernel', '4.2.2', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'modulename': 'IPython', -- GitLab From 31d3406af466b7af5c2fa8c85af5e2e95c0612d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:07:17 +0200 Subject: [PATCH 0895/2403] add SQLite dep in Python 2.7.5 easyconfig --- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index b8e12d524c..7844382331 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('SQLite', '3.8.5'), # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -- GitLab From 2a80620861105a62c9dda56080ae9efff2a38dcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:25:34 +0200 Subject: [PATCH 0896/2403] drop explicit dep on SQLite, use %(pyver)s and %(pyshortver)s --- .../IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index deb444d50b..3aa3ecb170 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -7,6 +7,7 @@ easyblock = 'Bundle' name = 'IPython' version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -18,14 +19,8 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} -python = 'Python' -pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - dependencies = [ - (python, pyver), - ('SQLite', '3.8.5'), + ('Python', '2.7.5'), ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), ('testpath', '0.3', versionsuffix), ] @@ -141,11 +136,11 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/ipython'], - 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], } sanity_check_commands = [ -- GitLab From 8b6dae32e5e96d91f6f3ac3af5001e44c48cf7a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 13:36:43 +0200 Subject: [PATCH 0897/2403] don't hardcode versions in source templates for extensions --- .../i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index 3aa3ecb170..cc3235c707 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -90,11 +90,11 @@ exts_list = [ }), ('setuptools_scm', '1.10.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], - 'source_tmpl': 'setuptools_scm-1.10.1.tar.bz2', + 'source_tmpl': 'setuptools_scm-%(version)s.tar.bz2', }), ('simplegeneric', '0.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], - 'source_tmpl': 'simplegeneric-0.8.1.zip', + 'source_tmpl': 'simplegeneric-%(version)s.zip', }), ('path.py', '8.1.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], -- GitLab From 40d159d417f8257e8820be35477abdf1d873eac7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 19 May 2016 13:58:01 +0200 Subject: [PATCH 0898/2403] Add likwid 4.1.0 --- .../l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb | 33 ++++++++++++++ .../l/likwid/likwid-4.1.0-config-mk.patch | 43 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb new file mode 100644 index 0000000000..cda484e29c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.1.0' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] + +patches = ['likwid-%(version)s-config-mk.patch'] + +builddependencies = [('binutils', '2.25', '', ('GCCcore', '4.9.3'))] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +maxparallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch new file mode 100644 index 0000000000..735ec88bea --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-config-mk.patch @@ -0,0 +1,43 @@ +# Patches the build system +# Ward Poelmans +diff -ur likwid-likwid-4.1.0.orig/config.mk likwid-likwid-4.1.0/config.mk +--- likwid-likwid-4.1.0.orig/config.mk 2016-05-19 13:16:28.000000000 +0200 ++++ likwid-likwid-4.1.0/config.mk 2016-05-19 13:46:33.345284562 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++#PREFIX = /usr/local#NO SPACE + + ################################################################# + # Common users do not need to change values below this comment! # +@@ -33,7 +33,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -44,7 +44,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -71,8 +71,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 -- GitLab From 24083ad232dca9485aa4be1c83a4b964881437d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:05:28 +0200 Subject: [PATCH 0899/2403] add easyconfig IPython-4.2.0-intel-2016a-Python-2.7.11.eb --- ...IPython-4.2.0-intel-2016a-Python-2.7.11.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0b3b531cf3 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,144 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'IPython' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.8.2', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2016.2.28', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('jupyter_client', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools_scm', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('path.py', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/path.py/'], + 'modulename': 'path', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pickleshare', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' -- GitLab From 59986fa63491a504f0e21e652ca0ca661e125d60 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 19 May 2016 14:10:35 +0200 Subject: [PATCH 0900/2403] Fix filename --- ...ikwid-4.1.0-GCCCore-4.9.3.eb => likwid-4.1.0-GCCcore-4.9.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/likwid/{likwid-4.1.0-GCCCore-4.9.3.eb => likwid-4.1.0-GCCcore-4.9.3.eb} (100%) diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCCore-4.9.3.eb rename to easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb -- GitLab From ffea8d3c28fb854c18aacd99afe3733257c26717 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:16:18 +0200 Subject: [PATCH 0901/2403] modify easyconfig Maven-3.2.3.eb, modify easyconfig Maven-3.3.3.eb, add easyconfig Maven-3.3.9.eb --- easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb | 1 - easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb | 1 - easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb | 22 ++++++++++++++++++++ 3 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb index c78d5ecd63..ae08a0b454 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] - sanity_check_paths = { 'files': ["bin/mvn"], 'dirs': [], diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb index a18f09ae41..642c9d91d2 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] - sanity_check_paths = { 'files': ["bin/mvn"], 'dirs': [], diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb new file mode 100644 index 0000000000..f38f753af8 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.3.9' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['apache-maven-%(version)s-bin.tar.gz'] +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] + +sanity_check_paths = { + 'files': ["bin/mvn"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6e368670a4e2d50b06252cae0871853e408cc454 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 14:30:56 +0200 Subject: [PATCH 0902/2403] add easyconfig Hadoop-2.6.0-cdh5.7.0-native.eb, add easyconfig CMake-3.5.2.eb --- easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 22 ++++++++++++++ .../h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb | 30 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb new file mode 100644 index 0000000000..412e055df6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb new file mode 100644 index 0000000000..b5884a562e --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.7.0' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] + +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + +builddependencies = [ + ('Maven', '3.3.9'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.5.2'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3-2.25')), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' -- GitLab From 7de330213bf1ef16b9ecc5d3d981f6233a69e18f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 May 2016 17:17:14 +0200 Subject: [PATCH 0903/2403] add easyconfig Yade-1.20.0-intel-2016a-Python-2.7.11.eb, add easyconfig Qt-4.8.7-intel-2016a-GLib-2.48.0.eb, add easyconfig PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb, add easyconfig minieigen-0.5.3-intel-2016a-Python-2.7.11.eb, add easyconfig libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb, add easyconfig IPython-3.2.3-intel-2016a-Python-2.7.11.eb, add easyconfig GTS-0.7.6-intel-2016a.eb, add easyconfig GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb, add easyconfig Loki-0.1.7-intel-2016a.eb, add easyconfig matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb, add easyconfig freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb --- .../freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb | 40 ++++++++ .../GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb | 37 ++++++++ .../g/GTS/GTS-0.7.6-intel-2016a.eb | 25 +++++ ...IPython-3.2.3-intel-2016a-Python-2.7.11.eb | 94 +++++++++++++++++++ .../l/Loki/Loki-0.1.7-intel-2016a.eb | 24 +++++ ...QGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb | 23 +++++ ...ntel-2016a-Python-2.7.11-freetype-2.6.3.eb | 47 ++++++++++ ...nieigen-0.5.3-intel-2016a-Python-2.7.11.eb | 26 +++++ .../PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb | 30 ++++++ .../q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 27 ++++++ .../Yade-1.20.0-intel-2016a-Python-2.7.11.eb | 60 ++++++++++++ 11 files changed, 433 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..fceaa15cbb --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXrandr', '1.5.0'), + ('libXi', '1.7.6'), + ('Mesa', mesa_ver), +] + +configopts = ' -DX11_X11_LIB="$EBROOTLIBX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTLIBX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTLIBXEXT/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTLIBXRANDR/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTLIBXRANDR/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTLIBXIlib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTLIBXI/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3f9a18be1e --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXi', '1.7.6'), + ('libXmu', '1.1.2'), + ('Mesa', mesa_ver), + ('libGLU', '9.0.0', versionsuffix), + ('freeglut', '3.0.0', versionsuffix), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb new file mode 100644 index 0000000000..fa9873619a --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b9c58c257f --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,94 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.2.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('pysqlite', '2.8.1', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('backports.ssl_match_hostname', '3.5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/'], + }), + ('certifi', '2015.11.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb new file mode 100644 index 0000000000..353bbfd940 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..3e6a70b031 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016a-Mesa-11.2.1.eb @@ -0,0 +1,23 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('libGLU', '9.0.0', versionsuffix), +] + +builddependencies = [('Qt', '4.8.7', '-GLib-2.48.0')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb new file mode 100644 index 0000000000..85c6625096 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +freetype_ver = '2.6.3' +versionsuffix = '-Python-%%(pyver)s-freetype-%s' % freetype_ver + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', freetype_ver), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..32173fca1a --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('Eigen', '3.2.7'), + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7383e08e64 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('GLib', '2.48.0'), + ('GTS' ,'0.7.6'), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..ada4c2ab36 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -0,0 +1,27 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +glib_ver = '2.48.0' +versionsuffix = '-GLib-%s' % glib_ver + +dependencies = [ + ('GLib', glib_ver), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXrender', '0.9.9'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..cecf209b8a --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '1.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +mesaver = '11.2.1' +dependencies = [ + ('Boost', '1.60.0', versionsuffix), + ('CGAL', '4.8', versionsuffix), + ('Eigen', '3.2.7'), + ('GDB', '7.10.1', versionsuffix), + ('GL2PS', '1.3.9', '-Mesa-%s' % mesaver), + ('GTS', '0.7.6'), + ('IPython', '3.2.3', versionsuffix), + ('libQGLViewer', '2.6.3', '-Mesa-%s' % mesaver), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.11'), + ('Qt', '4.8.7', '-GLib-2.48.0'), + ('SQLite', '3.9.2'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From fad10b526d2974383d5ef3e840c431c976e78df6 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 20 May 2016 11:58:49 +0200 Subject: [PATCH 0904/2403] add easyconfig Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb --- .../Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..61ca6bdf28 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), + ('cURL', '7.44.0'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.23.4', { + 'source_urls': ['http://cython.org/release/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'bio' -- GitLab From dde9b3d04fa8f6bd4005ba98c8ef9727dad8a0dd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 20 May 2016 12:33:19 +0200 Subject: [PATCH 0905/2403] Boost 1.60 without Python --- .../b/Boost/Boost-1.60.0-intel-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb new file mode 100644 index 0000000000..c6b8b5f02f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.60.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From bfe9230346a9a22c61b0b49c5f04ee3aefdd5bce Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 20 May 2016 12:33:46 +0200 Subject: [PATCH 0906/2403] GROMACS 5.1.2 for intel/2016a --- .../GROMACS-5.1.2-intel-2016a-hybrid.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb new file mode 100644 index 0000000000..1d0b356a9e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' -- GitLab From 218d926848f15ab39e8d32f6b80d79d3c30f1ddc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 20 May 2016 13:21:39 +0200 Subject: [PATCH 0907/2403] Python-2.7.11-goolf-1.7.20.eb and dependencies --- .../g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 30 ++++ .../libreadline-6.2-goolf-1.7.20.eb | 30 ++++ .../p/Python/Python-2.7.11-goolf-1.7.20.eb | 137 ++++++++++++++++++ .../s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb | 40 +++++ .../easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb | 25 ++++ 5 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..7a5dd73b3c --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215', '', True), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..be707f2f9d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb new file mode 100644 index 0000000000..244af3a298 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -0,0 +1,137 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.4' +scipyversion = '0.17.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + #('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4'), + ('GMP', '6.1.0'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.4', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..5b3197813b --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..b613bb1182 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 20344e023efd16e234068988d34a357d4fed7f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 May 2016 13:38:44 +0200 Subject: [PATCH 0908/2403] {bio}[intel/2016a] MRtrix 0.3.14 --- ...MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb | 26 ++++++++++++ .../m/MRtrix/MRtrix-0.3.14_intel-fixes.patch | 41 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..020ed91a4c --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'MRtrix' +version = '0.3.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +#patches = ['MRtrix-%(version)s.patch'] +patches = ['MRtrix-%(version)s_intel-fixes.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.11'), + ('Mesa', '11.2.1'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch new file mode 100644 index 0000000000..bbc46048db --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.14_intel-fixes.patch @@ -0,0 +1,41 @@ +fix compilation with Intel compilers, cfr. https://github.com/MRtrix3/mrtrix3/pull/622 +author: Kenneth Hoste (HPC-UGent) +diff --git a/src/dwi/tractography/seeding/base.h b/src/dwi/tractography/seeding/base.h +--- a/src/dwi/tractography/seeding/base.h ++++ b/src/dwi/tractography/seeding/base.h +@@ -62,7 +62,7 @@ namespace MR + uint32_t get_count (ImageType& data) + { + std::atomic count (0); +- ThreadedLoop (data).run ([&] (decltype(data)& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); ++ ThreadedLoop (data).run ([&] (ImageType& v) { if (v.value()) count.fetch_add (1, std::memory_order_relaxed); }, data); + return count; + } + + +diff --git a/lib/adapter/base.h b/lib/adapter/base.h +--- a/lib/adapter/base.h ++++ b/lib/adapter/base.h +@@ -25,7 +25,7 @@ namespace MR + namespace Adapter + { + +- template