From aebbce71060aa1e9f057be19954f6d8f39e7e2a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:45:22 +0100 Subject: [PATCH 0001/1172] add easyconfig file for Vampir --- .../v/Vampir/Vampir-8.1.0-linux-x86_64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb new file mode 100644 index 0000000000..933876ab64 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb @@ -0,0 +1,32 @@ +# 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='Binary' + +name = "Vampir" +version = "8.1.0" +versionsuffix = "-linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s-standard%s-setup.bin' % (version, versionsuffix)] + +install_cmd = "./vampir-8.1.0-standard-linux-x86_64-setup.bin --silent --instdir=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From c960524a9568dfad8922bc648a0563776395f0d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Nov 2013 21:39:37 +0100 Subject: [PATCH 0002/1172] get rid of hardcoding version/versionsuffix --- easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb index 933876ab64..7b467d1272 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb @@ -20,9 +20,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['vampir-%s-standard%s-setup.bin' % (version, versionsuffix)] +sources = ['vampir-%(version)s-standard%(versionsuffix)s-setup.bin'] -install_cmd = "./vampir-8.1.0-standard-linux-x86_64-setup.bin --silent --instdir=%(installdir)s" +install_cmd = "./vampir-%(version)s-standard%(versionsuffix)s-setup.bin --silent --instdir=%(installdir)s" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], -- GitLab From e690eec2d9aa50c46603d8801860b05023005eea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Dec 2013 17:27:45 +0100 Subject: [PATCH 0003/1172] add easyconfig files for ncdf/ncdf4 for R 2.15.3 + dep easyconfigs --- ...HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb | 31 +++++++++++++++++++ .../n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb | 29 +++++++++++++++++ .../ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb | 29 +++++++++++++++++ .../netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb | 21 +++++++++++++ 4 files changed, 110 insertions(+) create mode 100755 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb create mode 100644 easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb create mode 100755 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb new file mode 100755 index 0000000000..1b26514524 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb @@ -0,0 +1,31 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '5.3.0'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +zlib = 'zlib' +zlibver = '1.2.5' +versionsuffix += '-%s-%s' % (zlib, zlibver) + +dependencies = [ + (zlib, zlibver), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000..a5891cb70a --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf' +version = '1.6.6' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000..dc58f15fe2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.10' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb new file mode 100755 index 0000000000..5c53c8bf57 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +version = '4.2.1.1' +versionsuffix = '-zlib-1.2.5' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [ + ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), + ('Doxygen', '1.8.2'), +] + +moduleclass = 'data' -- GitLab From 4b67659ba2376c552748309970b0583135fb85af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 16:58:30 +0100 Subject: [PATCH 0004/1172] add patch file required for correct CUDA-aware OpenMPI v1.7.3 build --- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 2 ++ .../OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch | 16 ++++++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 9198983666..4ddc24fe07 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +patches = ['OpenMPI-%(version)s_common-cuda-lib.patch'] + builddependencies = [ ('Automake', '1.14'), ('Autoconf', '2.69') diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch new file mode 100644 index 0000000000..4ba9ebab68 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch @@ -0,0 +1,16 @@ +see http://permalink.gmane.org/gmane.comp.clustering.open-mpi.user/20404, +patch obtained via https://svn.open-mpi.org/trac/ompi/changeset/29762 +Index: /branches/v1.7/ompi/mca/pml/ob1/Makefile.am +=================================================================== +--- /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29624) ++++ /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29762) +@@ -68,4 +68,9 @@ + mca_pml_ob1_la_LDFLAGS = -module -avoid-version + ++if OPAL_cuda_support ++mca_pml_ob1_la_LIBADD = \ ++ $(top_ompi_builddir)/ompi/mca/common/cuda/libmca_common_cuda.la ++endif ++ + noinst_LTLIBRARIES = $(component_noinst) + libmca_pml_ob1_la_SOURCES = $(ob1_sources) -- GitLab From b9b0d39cf997b2d2d74d557f36a2a58ff8125d63 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 4 Feb 2014 16:38:19 +0100 Subject: [PATCH 0005/1172] CONTRAfold-2.02-goolf-1.4.10.eb --- .../CONTRAfold-2.02-goolf-1.4.10.eb | 31 +++++++++++++++++++ .../c/CONTRAfold/contrafold-gcc47.patch | 20 ++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb new file mode 100644 index 0000000000..815406dfba --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAfold' +version = '2.02' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contrafold/' +description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_'))] + +patches = ['contrafold-gcc47.patch'] + +start_dir = 'src' + +files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/score_prediction', 'bin/contrafold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch new file mode 100644 index 0000000000..d484c76bfd --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch @@ -0,0 +1,20 @@ +--- contrafold.orig/src/Makefile 2008-08-14 02:08:30.000000000 +0200 ++++ contrafold/src/Makefile 2014-02-04 13:51:29.041589171 +0100 +@@ -1,6 +1,6 @@ + CXX = g++ + +-CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall ++CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall -fpermissive + LINKFLAGS = -lm + GDLINKFLAGS = -lgd -lpng + +--- contrafold.orig/src/Utilities.cpp 2008-08-14 02:08:31.000000000 +0200 ++++ contrafold/src/Utilities.cpp 2014-02-04 14:09:09.082650184 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; -- GitLab From 13b7f5c9ee8638fed92150ab57cdb6467b8320df Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Mon, 10 Feb 2014 23:48:22 +0100 Subject: [PATCH 0006/1172] contrib blasr configs. --- .../b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb | 43 +++++++++++++++++++ .../easyconfigs/b/blasr/non-static.patch | 13 ++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/blasr/non-static.patch diff --git a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..5663de6022 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb @@ -0,0 +1,43 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +name = 'blasr' +version = 'smrtanalysis-2.1' + +easyblock = "MakeCp" + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +#like https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz for tag smnrtanalysis +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + + +patches = ['non-static.patch'] + +files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] + + +sanity_check_paths = { + 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', 'bin/guidedalign', 'bin/pbmask'], + 'dirs': [], +} + +makeopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/non-static.patch b/easybuild/easyconfigs/b/blasr/non-static.patch new file mode 100644 index 0000000000..03b7b3f2bb --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/non-static.patch @@ -0,0 +1,13 @@ +--- common.mk.orig 2013-11-08 15:19:36.848815000 +0100 ++++ common.mk 2013-11-08 15:19:54.854217000 +0100 +@@ -24,6 +24,7 @@ + ifeq ($(shell $(CC) -dumpversion | awk -F '.' '$$1*100+$$2>404{print "yes"}'),yes) + CPPOPTS += -fpermissive + endif +-ifneq ($(shell uname -s),Darwin) +- STATIC = -static +-endif ++# Why oh why ... ++#ifneq ($(shell uname -s),Darwin) ++# STATIC = -static ++#endif -- GitLab From ee0ac46ff9ae257f194baf35407fd7aa23ae391f Mon Sep 17 00:00:00 2001 From: build Date: Fri, 28 Feb 2014 14:09:44 +0200 Subject: [PATCH 0007/1172] Contributing parallel version of ABINIT built with ETSF_IO to enable checkpointing --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..c1d2b559d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..7e1b945d47 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + -- GitLab From 64bae018eaecad71608473c16bd9f0c97031b21c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 17:03:31 +0100 Subject: [PATCH 0008/1172] add easyconfig file for LAMARC + required patch file --- .../l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb | 23 +++++++++++++++++++ .../l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch | 10 ++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb new file mode 100644 index 0000000000..742fe0d215 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +name = 'LAMARC' +version = '2.1.9' +versionsuffix = '-headless' + +homepage = 'http://evolution.genetics.washington.edu/lamarc/' +description = """LAMARC is a program which estimates population-genetic parameters such as population size, + population growth rate, recombination rate, and migration rates.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://evolution.genetics.washington.edu/lamarc/download/'] +sources = ['%(namelower)s-%(version)s-src.tgz'] + +patches = ['LAMARC-2.1.9_Makefile-fix.patch'] + +configopts = "--disable-converter --disable-gui" + +sanity_check_paths = { + 'files': ["bin/lamarc"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch new file mode 100644 index 0000000000..74db39ff1c --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch @@ -0,0 +1,10 @@ +--- lamarc/Makefile.in.orig 2014-03-19 14:25:08.261820031 +0100 ++++ lamarc/Makefile.in 2014-03-19 14:25:15.382031107 +0100 +@@ -1810,7 +1810,6 @@ + doc/html/genotype.html \ + doc/html/glossary.html \ + doc/html/growthmenu.html \ +- doc/html/forces.html \ + doc/html/index.html \ + doc/html/insumfile.2reg3rep.html \ + doc/html/insumfile.2reg3rep.xml \ -- GitLab From ae32b280a9f5cd19f8b2df995ee60303de9545ce Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 5 Apr 2014 16:41:37 +0200 Subject: [PATCH 0009/1172] AutoDock_Vina-1.1.2-linux_x86.eb --- .../AutoDock_Vina-1.1.2-linux_x86.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb new file mode 100644 index 0000000000..a27cf3bd19 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.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 = "Tarball" + +name = 'AutoDock_Vina' +version = '1.1.2' +versionsuffix = '_linux_x86' + +homepage = 'http://vina.scripps.edu/index.html' +description = """ AutoDock Vina is an open-source program for doing molecular docking. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://vina.scripps.edu/download/'] +sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.','_'), versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/vina_split", "bin/vina"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 2aab27e19259b38b61250c798f1897d07e5c2140 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 8 Apr 2014 23:21:18 +0200 Subject: [PATCH 0010/1172] Check-0.9.12-goolf-1.4.10.eb --- .../c/Check/Check-0.9.12-goolf-1.4.10.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb new file mode 100644 index 0000000000..e63d0852ef --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +# 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 = "Check" +version = "0.9.12" + +homepage = 'http://check.sourceforge.net' +description = """ Check is a unit testing framework for C. It features a simple interface + for defining unit tests, putting little in the way of the developer. Tests are run in a + separate address space, so both assertion failures and code errors that cause segmentation + faults or other signals can be caught. Test results are reportable in the following: + Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' -- GitLab From 0d7fbaff77990066bd537a1ada4fa77fa96bd838 Mon Sep 17 00:00:00 2001 From: Andreas Panteli Date: Fri, 11 Apr 2014 12:16:01 +0300 Subject: [PATCH 0011/1172] Contribute Perl module Parallel-ForkManager --- ...rkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..b35839d741 --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli +# License:: MIT/GPL +# +## + +easyblock = 'PerlModule' + +name = 'Parallel-ForkManager' +version = '1.06' + +homepage = 'http://search.cpan.org/~szabgab/Parallel-ForkManager-1.06/lib/Parallel/ForkManager.pm' +description = """A simple parallel processing fork manager""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver) +] + +options = {'modulename': 'Parallel::ForkManager'} + +moduleclass = 'data' -- GitLab From 82ad16ec61eda751ad121612655afb7d8ca85319 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 14 Apr 2014 19:25:24 +0200 Subject: [PATCH 0012/1172] IMPUTE2 2.3.0 easyconfigs --- .../i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb | 32 +++++++++++++++++++ .../i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb new file mode 100644 index 0000000000..0c2d1cc059 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.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 = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_dynamic' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb new file mode 100644 index 0000000000..0fb795f7eb --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.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 = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_static' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + -- GitLab From 39d83236d6a13adfea9314c797672ad40a157ee0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 May 2013 21:29:02 +0200 Subject: [PATCH 0013/1172] readd MariaDB goolf/goalf easyconfigs removed in #217 --- .../MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb | 27 +++++++++++++++++++ .../m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb | 27 +++++++++++++++++++ .../m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb | 1 + 3 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..4615fe660c --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '5.5.29' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'goalf' , 'version': '1.1.0-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('ncurses' , '5.9'), +] + +builddependencies = [ + ('CMake', '2.8.4'), +] + +configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +makeopts = "VERBOSE=1" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb new file mode 100644 index 0000000000..89c5e0ba20 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '5.5.29' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'goolf' , 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('ncurses' , '5.9'), +] + +builddependencies = [ + ('CMake', '2.8.4'), +] + +configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +makeopts = "VERBOSE=1" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb index ec819fe6b6..6d5a199225 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb @@ -29,3 +29,4 @@ sanity_check_paths = { } moduleclass = 'data' +======= -- GitLab From 13a31a1ba2f7b3ce9b3593d85af03f450a1363a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Apr 2014 09:18:08 +0200 Subject: [PATCH 0014/1172] add easyconfig files for IMa2 --- .../i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb | 23 +++++++++++++++++++ .../i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100755 easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb create mode 100755 easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb new file mode 100755 index 0000000000..690d220498 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb new file mode 100755 index 0000000000..a3ed62f5d6 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6af8de3001d1c136b9f5456ce61399f30a81284e Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 19 May 2014 14:07:41 +0200 Subject: [PATCH 0015/1172] CUDA-6.0.37.eb --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 29 +++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb new file mode 100644 index 0000000000..f6e34de664 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.0.37' + +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'} + +# eg. http://developer.download.nvidia.com/compute/cuda/5_0/rel-update-1/installers/cuda_5.0.35_linux_64_rhel5.x-1.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_0/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] + +moduleclass = 'system' -- GitLab From 47b95ac76e0393c0c7bb47ad786e8e62dda7d1e3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 19 May 2014 14:20:43 +0200 Subject: [PATCH 0016/1172] added %(version_minor)s to source_urls updated the download url example --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index f6e34de664..0ebf372eeb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -21,9 +21,8 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. http://developer.download.nvidia.com/compute/cuda/5_0/rel-update-1/installers/cuda_5.0.35_linux_64_rhel5.x-1.run -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_0/rel/installers/'] - +# http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] moduleclass = 'system' -- GitLab From 1078dea61a9a624e1907bb7eb7b6a78c3b0e609d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Jun 2014 16:13:41 +0200 Subject: [PATCH 0017/1172] add easyconfig for ADF --- .../a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb new file mode 100755 index 0000000000..6395f17b38 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = "ADF" +version = '2009.01a.pc64_linux.intelmpi' + +homepage = 'http://www.scm.com/' +description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s.bin.tgz'] + +dependencies = [('impi', '3.2.2.006')] + +sanity_check_paths = { + 'files': ['bin/adf', 'bin/adf.exe'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 20f4e3e6279fe5d8de7f4ebc87b77d16944155cf Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 4 Jul 2014 16:10:41 +1200 Subject: [PATCH 0018/1172] new toolchain release added --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 8 ++-- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb | 23 +++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb | 23 +++++++++++ .../OpenMPI-1.6.5-iccifort-2011.13.367.eb | 38 ++++++++++++++++++ .../OpenMPI-1.6.5-iccifort-2013.4.183.eb | 39 +++++++++++++++++++ 6 files changed, 127 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index 0db4c8f64f..dfb97e3568 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,14 +9,12 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' +sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] # deps for interface build dependencies = [ - ('icc', compver), - ('ifort', compver), + ('icc', '2011.13.367'), + ('ifort', '2011.13.367'), ('impi', '4.1.0.027'), ] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 839fe8f604..d074eeb0ea 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_mpi_p_%(version)s.tgz'] +sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb new file mode 100644 index 0000000000..6a4ff077e3 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '6.5.4' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2013.4.183' +comp = ('iccifort', compver) +ompi = 'OpenMPI' +ompiver = '1.6.5' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (ompi, ompiver, '', comp), + ('imkl', '11.0.4.183', '-%s-%s' % (ompi, ompiver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb new file mode 100644 index 0000000000..1d73c1141d --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '6.7.2' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2013.4.183' +comp = ('iccifort', compver) +ompi = 'OpenMPI' +ompiver = '1.6.5' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (ompi, ompiver, '', comp), + ('imkl', '11.1.2.144', '-%s-%s' % (ompi, ompiver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb new file mode 100644 index 0000000000..17ecb57b0f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb @@ -0,0 +1,38 @@ +name = 'OpenMPI' +version = '1.6.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2011.13.367'} + +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-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +dependencies = [('hwloc', '1.6')] + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", "otf", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb new file mode 100644 index 0000000000..29075bd3b2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb @@ -0,0 +1,39 @@ +name = 'OpenMPI' +version = '1.6.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2013.4.183'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib --with-pmi ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +dependencies = [('hwloc', '1.8.1')] + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 0063db32993fb4a1c4418ce7019fad1d5d57b1f9 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:40:05 +0300 Subject: [PATCH 0019/1172] Adding ABINIT v.7.4.3 with dummy and goolf (parallel version) toolchains --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 +++++++++++++++++++ .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 ++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..a3fe29c410 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb new file mode 100644 index 0000000000..fb4d81965f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'ABINIT' +version = '7.4.3' +versionsuffix = '-x86_64_linux_gnu4.5' + +altversions = ['7.0.3', '7.0.4', '7.0.5'] + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] +source_urls = ['http://ftp.abinit.org/'] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..350da2d908 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + +moduleclass = 'chem' -- GitLab From 38d072b44abb10c2bde6d7309c5a4466508f3040 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:45:37 +0300 Subject: [PATCH 0020/1172] Adding Bismark --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..d749578a18 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'Bismark' +version = '0.10.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] + + +dependencies = [ + ('Bowtie2', '2.0.2'), +] + +sanity_check_paths = { + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From 845d1d8b8f8a44557e47d3220fb32db7cbba3162 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:38:12 +0300 Subject: [PATCH 0021/1172] Contributing DendroPy --- ...ndroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d3ec591256 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,37 @@ +## +#This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = "PythonPackage" + +name = 'DendroPy' +version = '3.12.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. +""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] +sources = ['%s-%s.tar.gz' % (name, version)] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 34502fa5a0e9134260060cedb4af99061fa9c5d4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:43:38 +0300 Subject: [PATCH 0022/1172] Contrib GATK v.3.0.0 --- .../g/GATK/GATK-3.0-0-Java-1.7.0_10.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb new file mode 100644 index 0000000000..13de380c1b --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# 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 = 'Tarball' + +name = 'GATK' +version = '3.0-0' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 7e3847fec5f46ecd5d41316da6410ae195213d3e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 13:57:50 +0300 Subject: [PATCH 0023/1172] Contributing picard version 1.109 --- easybuild/easyconfigs/p/picard/picard-1.109.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.109.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb new file mode 100644 index 0000000000..b02c4dfde3 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.109' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_10')] + +moduleclass = 'bio' -- GitLab From a3ace75a4d542b028c8ba863fd3129f92f6ea5f7 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 13:59:59 +0300 Subject: [PATCH 0024/1172] Contrib Theano v.0.6.0 --- .../Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 30 ++++++++++++++++++ .../Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 31 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..8308ab148a --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions +involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] + } + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..1e72223824 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions + involving multi-dimensional arrays efficiently.""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] + } + +moduleclass = 'math' -- GitLab From bd66b7e4bf46f52756c4199c803b5abab82f7a4e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:09:32 +0300 Subject: [PATCH 0025/1172] Contributing MAT I/O Library --- .../m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..99d44c6862 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'MATIO' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s-%s.zip' % (name.lower(), version)] + + +dependencies = [('zlib','1.2.7'), +] + +moduleclass = 'lib' -- GitLab From 371e47ed5886ebab9ea8c6f25b448b4d7bf15ef4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:14:23 +0300 Subject: [PATCH 0026/1172] Contributing Tk v8.6.1 --- .../easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb 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 new file mode 100644 index 0000000000..334b02c101 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'Tk' +version = '8.6.1' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%s%s-src.tar.gz' % (name.lower(), version)] + +dependencies = [('Tcl', version)] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From c2c5d304ff9411b2a303bd6e3e05a319a0e618ed Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:18:01 +0300 Subject: [PATCH 0027/1172] Contributing PROJ Cartographic Projections Library --- .../p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 26 +++++++++++++++++ .../p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..d3034c9b33 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://download.osgeo.org/proj/'] + +sanity_check_paths = { + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], + +} diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..618aab840c --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://download.osgeo.org/proj/'] + +sanity_check_paths = { + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], + +} + + -- GitLab From c76f17999c613ea2a5eb6647454d1d21bd3bc3d3 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:31:36 +0300 Subject: [PATCH 0028/1172] Contributing pBWA --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb new file mode 100644 index 0000000000..754be559e1 --- /dev/null +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "MakeCp" + +name = 'pBWA' +version = '0.5.9_1.21009' + +homepage = 'http://pbwa.sourceforge.net/' +description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s_%(version)s.zip'] +source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] + + + +dependencies = [ + ('BWA', '0.7.4'), +] + +files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], + +} + +moduleclass = 'bio' -- GitLab From 5c525705338558ca807cb3a8cab284a02f714309 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 7 Aug 2014 14:49:43 +0300 Subject: [PATCH 0029/1172] Minor changes to config files --- .../easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 8 ++++---- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 10 ++++------ 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index d3034c9b33..52eec6cca7 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -11,7 +11,8 @@ name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' -description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" +description = """Program proj is a standard Unix filter function which converts + geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -20,7 +21,6 @@ sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], - 'dirs': [], - + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], } diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 618aab840c..f62a689830 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -11,7 +11,8 @@ name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' -description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" +description = """Program proj is a standard Unix filter function which converts + geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -20,9 +21,6 @@ sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], - 'dirs': [], - + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], } - - -- GitLab From 3c3004285127ac62d3e5b2158b6834739a930a40 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 7 Aug 2014 15:04:45 +0300 Subject: [PATCH 0030/1172] A few more changes --- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 52eec6cca7..4661417502 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -17,8 +17,8 @@ description = """Program proj is a standard Unix filter function which converts toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index f62a689830..589656723f 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -17,8 +17,8 @@ description = """Program proj is a standard Unix filter function which converts toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], -- GitLab From 12de7b508c63a9ee2395608700c534cc3bd8edc1 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 14 Aug 2014 15:30:05 +1200 Subject: [PATCH 0031/1172] Score-P goolf-1.5.14 --- .../c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 35 +++++++++++++++ .../o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 26 +++++++++++ .../p/PDT/PDT-3.20-goolf-1.5.14.eb | 45 +++++++++++++++++++ .../s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 39 ++++++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..8bc6ecb55a --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.2.3" + +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': 'goolf', 'version': '1.5.14'} + +# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] + +patches = ['Cube-4.2_fix-Qt-version-check.patch'] + +dependencies = [('Qt', '4.8.4')] + +configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..c2bd8f4970 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -0,0 +1,26 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +name = "OPARI2" +version = "1.1.2" + +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': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb new file mode 100644 index 0000000000..1933e4066b --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -0,0 +1,45 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +name = "PDT" +version = "3.20" + +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': 'goolf', 'version': '1.5.14'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..196dc0e191 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = "Score-P" +version = "1.2.3" + +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': 'goolf', 'version': '1.5.14'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22'), + ('Cube', '4.2.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.20'), +] + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 659dca6f9820e2e88f218586eaf1cf1687788377 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 14 Aug 2014 16:59:41 +1200 Subject: [PATCH 0032/1172] missing dependencies --- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 33 ++++++++++++++ .../o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 31 +++++++++++++ .../p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb | 44 +++++++++++++++++++ .../easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb | 17 +++++++ 4 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb 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 new file mode 100644 index 0000000000..e4a2454e0e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.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 = [GNU_SOURCE] + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +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/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..e0a03c63d3 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.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/ +## +easyblock = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.2.1" + +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 will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..f1dcf6fbfe --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -0,0 +1,44 @@ +## +# 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 = 'PAPI' +version = '5.2.0' + +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': 'goolf', 'version': '1.5.14'} + +# 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' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..e0d6a9d420 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' -- GitLab From 84c026aa0326b20a09e0f53a6d7431b691369548 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 15 Aug 2014 15:41:43 +1200 Subject: [PATCH 0033/1172] minor changes --- easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index 8bc6ecb55a..3628401ad4 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -21,8 +21,6 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] -patches = ['Cube-4.2_fix-Qt-version-check.patch'] - dependencies = [('Qt', '4.8.4')] configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" -- GitLab From 7f2076dcc517dcac3b51742cc86ddb20cc274adf Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:51:55 +1200 Subject: [PATCH 0034/1172] Delete imkl-10.3.12.361.eb --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb deleted file mode 100644 index dfb97e3568..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'imkl' -version = '10.3.12.361' - -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': 'dummy', 'version': 'dummy'} - -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] - -# deps for interface build -dependencies = [ - ('icc', '2011.13.367'), - ('ifort', '2011.13.367'), - ('impi', '4.1.0.027'), -] - -dontcreateinstalldir = 'True' - -interfaces = True - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'numlib' -- GitLab From 83ac4560b153fbadb3103c3cfb7b7efdb3691444 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:52:45 +1200 Subject: [PATCH 0035/1172] Delete impi-4.1.0.027.eb --- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb deleted file mode 100644 index d074eeb0ea..0000000000 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'impi' -version = '4.1.0.027' - -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': 'dummy', 'version': 'dummy'} - -sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] - -dontcreateinstalldir = 'True' - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'mpi' -- GitLab From 2cd359ce10c48b88098b66a755b91b9b0f5e9f92 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:53:23 +1200 Subject: [PATCH 0036/1172] Delete iomkl-6.5.4.eb --- easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb | 23 -------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb deleted file mode 100644 index 6a4ff077e3..0000000000 --- a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'iomkl' -version = '6.5.4' - -homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compver = '2013.4.183' -comp = ('iccifort', compver) -ompi = 'OpenMPI' -ompiver = '1.6.5' - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (ompi, ompiver, '', comp), - ('imkl', '11.0.4.183', '-%s-%s' % (ompi, ompiver)), -] - -moduleclass = 'toolchain' -- GitLab From 18d8c907244260a2ee1c496ad781e1bb7b49e5ee Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:53:35 +1200 Subject: [PATCH 0037/1172] Delete iomkl-6.7.2.eb --- easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb | 23 -------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb deleted file mode 100644 index 1d73c1141d..0000000000 --- a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'iomkl' -version = '6.7.2' - -homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compver = '2013.4.183' -comp = ('iccifort', compver) -ompi = 'OpenMPI' -ompiver = '1.6.5' - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (ompi, ompiver, '', comp), - ('imkl', '11.1.2.144', '-%s-%s' % (ompi, ompiver)), -] - -moduleclass = 'toolchain' -- GitLab From ad4b011978294898c2df6b06b3a3136f4f449e51 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:54:41 +1200 Subject: [PATCH 0038/1172] Delete OpenMPI-1.6.5-iccifort-2011.13.367.eb --- .../OpenMPI-1.6.5-iccifort-2011.13.367.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb deleted file mode 100644 index 17ecb57b0f..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'OpenMPI' -version = '1.6.5' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'iccifort', 'version': '2011.13.367'} - -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-openib ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support - -dependencies = [('hwloc', '1.6')] - -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' -- GitLab From 75ea4b4daf3d4a3556766f4a8dac11f9dd519cb6 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:54:57 +1200 Subject: [PATCH 0039/1172] Delete OpenMPI-1.6.5-iccifort-2013.4.183.eb --- .../OpenMPI-1.6.5-iccifort-2013.4.183.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb deleted file mode 100644 index 29075bd3b2..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'OpenMPI' -version = '1.6.5' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'iccifort', 'version': '2013.4.183'} - -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-openib --with-pmi ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support - -dependencies = [('hwloc', '1.8.1')] - -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' -- GitLab From fec5c07c530a026d72130cac630ff7c57868c4ce Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 15 Aug 2014 16:00:57 +1200 Subject: [PATCH 0040/1172] minor change --- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index dfb97e3568..9b7df526e4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] +sources = ['l_mkl_%(version)s_intel64.tgz'] # deps for interface build dependencies = [ -- GitLab From a1504d145f576f88b72041cb493de6834baffccf Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 23 Aug 2014 17:36:26 +0200 Subject: [PATCH 0041/1172] PBZIP2 easyconfigs goolf and ictce --- .../easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb | 34 +++++++++++++++++++ .../p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb new file mode 100644 index 0000000000..e0710326fb --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/1.1.8-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 = 'PBZIP2' +version = '1.1.8' + +homepage = 'http://compression.ca/pbzip2/' +description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file + compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output + of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed + with pbzip2 can be decompressed with bzip2).""" + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['http://compression.ca/pbzip2/'] +sources = [SOURCELOWER_TAR_GZ] + +makeopts = ' CC=$CXX' + +parallel = 1 + +files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] + +sanity_check_paths = { + 'files': ["bin/pbzip2"], + 'dirs': [""], +} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb new file mode 100644 index 0000000000..b66756cb0a --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.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 = 'PBZIP2' +version = '1.1.8' + +homepage = 'http://compression.ca/pbzip2/' +description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file + compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output + of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed + with pbzip2 can be decompressed with bzip2).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compression.ca/pbzip2/'] +sources = [SOURCELOWER_TAR_GZ] + +makeopts = ' CC=$CXX' + +parallel = 1 + +files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] + +sanity_check_paths = { + 'files': ["bin/pbzip2"], + 'dirs': [""], +} + +moduleclass = 'tools' + -- GitLab From 72844a75f940483df16c43574f9d7b2390a47ee4 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 23 Aug 2014 18:02:23 +0200 Subject: [PATCH 0042/1172] SSAHA2 easyconfigs for 64 and 32bits binaries --- .../easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb | 36 +++++++++++++++++++ .../s/SSAHA2/SSAHA2-2.5.5-x86_64.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb create mode 100644 easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb new file mode 100644 index 0000000000..bda774ae23 --- /dev/null +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.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 = "Tarball" + +name = 'SSAHA2' +version = '2.5.5' +versionsuffix = "_i686" + +homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' +description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a + pairwise sequence alignment program designed for the efficient mapping of sequencing + reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms + (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) + are supported. A pile-up pipeline for analysis and genotype calling is available as + a separate package. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] +sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] + +sanity_check_paths = { + 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb new file mode 100644 index 0000000000..2a4076857e --- /dev/null +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.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 = "Tarball" + +name = 'SSAHA2' +version = '2.5.5' +versionsuffix = "_x86_64" + +homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' +description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a + pairwise sequence alignment program designed for the efficient mapping of sequencing + reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms + (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) + are supported. A pile-up pipeline for analysis and genotype calling is available as + a separate package. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] +sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] + +sanity_check_paths = { + 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' + -- GitLab From 8b475b5b932795cbdf9d4fd509bbbbf075635bd6 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 23 Aug 2014 22:26:06 +0200 Subject: [PATCH 0043/1172] STAR goolf-1.4.10 --- .../s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../s/STAR/STAR_missing_includes.patch | 10 ++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb new file mode 100644 index 0000000000..aaedf45292 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-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 = 'STAR' +version = '2.3.0e' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://rna-star.googlecode.com/files/'] +sources = ['%(name)s_%(version)s.tgz'] + +patches = ['STAR_missing_includes.patch'] + +# a binary is provided with the source files. We delete it +premakeopts = 'rm STAR && ' + +parallel = 1 + +files_to_copy = [(["STAR"], "bin"), "README.txt"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [""], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch new file mode 100644 index 0000000000..82d8f2d8e0 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch @@ -0,0 +1,10 @@ +--- STAR_2.3.0e.orig/Genome.cpp 2013-01-22 21:51:14.000000000 +0100 ++++ STAR_2.3.0e/Genome.cpp 2014-08-23 22:06:02.954503545 +0200 +@@ -6,6 +6,7 @@ + #include "streamFuns.h" + #include + #include ++#include + + #define SHM_sizeG 0 + #define SHM_sizeSA 8 -- GitLab From 30ebeb7abc101c84a786e4eeec51b65cc80065db Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 24 Aug 2014 13:53:43 +0200 Subject: [PATCH 0044/1172] IDBA-UD-1.1.1-goolf-1.4.10.eb --- .../i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..43d9e4ed11 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +# 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 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in premakeopts +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.1' + +homepage = 'http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads + Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. + IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth + contigs are removed iteratively with cutoff threshold from low to high to reduce the errors + in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled + locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD + can iterate k value of de Bruijn graph to a very large value with less gaps and less branches + to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://hku-idba.googlecode.com/files/'] +sources = ['idba-%(version)s.tar.gz'] + +premakeopts = './configure && ' + +# we delete every .o file which is left in bin folder +makeopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' + +files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' + -- GitLab From 30e0006a8e2c9f614bdfec4d2c2b8e3b3b28a4cd Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Sep 2014 18:19:13 +0200 Subject: [PATCH 0045/1172] added tabbix easyonfigs --- .../t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 36 +++++++++++++++++++ .../t/tabix/tabix-0.2.6-intel-2014b.eb | 30 ++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..175efc7a74 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-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='MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb new file mode 100644 index 0000000000..2f4bddea4e --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -0,0 +1,30 @@ +easyblock='MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From 97176bfc0696547a7a6314bf0a66c41e075c77b7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 10:39:30 +0200 Subject: [PATCH 0046/1172] PostgreSQL with Perl binding --- .../DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 26 ++++++++++++ .../PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb | 41 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..5caf1511aa --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'DBD-Pg' +version = '3.4.1' + +homepage = 'http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/' +description = """Perl binding for PostgreSQL""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5"), +] + + +options = {'modulename': 'DBD::Pg'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb new file mode 100644 index 0000000000..9b40199a4f --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb @@ -0,0 +1,41 @@ +name = 'PostgreSQL' +version = '9.3.5' + +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': '2014b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.7.0_60' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('Perl', '5.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 36aa12e557164986ff49d4fced15e9c03dd44d09 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 14:27:46 +0200 Subject: [PATCH 0047/1172] Typo Corrected --- ...geSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgeSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} (100%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb -- GitLab From 0943e87b0ea092d881f2b7e5d7bc6cfa15cde0f1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 8 Sep 2014 12:49:29 +0200 Subject: [PATCH 0048/1172] updated download urls --- .../b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- .../b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb | 4 ++-- .../b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb index e0f3e3aa78..e3bd679270 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb index 772e359455..d030d9efdd 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb index 644fe3ba68..f1be6ce30a 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' -- GitLab From e7c3b62cd358037b8d85cd6d4a3ced20c84540d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:24 +0200 Subject: [PATCH 0049/1172] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 5caf1511aa..8e07224960 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,10 +15,7 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [ - (perl, perlver), - ("PostgreSQL", "9.3.5"), -] +dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] options = {'modulename': 'DBD::Pg'} -- GitLab From c62fc4a88b50b63e1461f8b02a5d045b31cdf85a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:34 +0200 Subject: [PATCH 0050/1172] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 8e07224960..ca812f75ef 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -17,7 +17,6 @@ versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] - options = {'modulename': 'DBD::Pg'} moduleclass = 'data' -- GitLab From d0e3c5a86c5e372ac14c4d2a4f54aa22e7ad02a4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 Sep 2014 10:40:06 +0200 Subject: [PATCH 0051/1172] CUDA 6.5.14 --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 29 +++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb new file mode 100644 index 0000000000..2698ca5e91 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.5.14' + +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'} + +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] + +moduleclass = 'system' -- GitLab From 4ee9183cb074fa0e245949a0c797c109057eaa9f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 22 Sep 2014 17:43:17 +0200 Subject: [PATCH 0052/1172] added tecplot easyconfig --- .../t/tecplot360ex/tecplot360ex.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb new file mode 100644 index 0000000000..08d437e5b8 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) +moduleclass = 'vis' + -- GitLab From a9ff525ef3cab6ff122bdc52f66e57bd3755efcb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:07:43 +0200 Subject: [PATCH 0053/1172] added ngsipce --- .../n/ngspice/ngspice-26-intel-2014b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb new file mode 100644 index 0000000000..371953f64b --- /dev/null +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -0,0 +1,26 @@ +name = 'ngspice' +version = '26' + +homepage = 'http://ngspice.sourceforge.net' +description = """Ngspice is a mixed-level/mixed-signal circuit simulator. Its code + is based on three open source software packages: Spice3f5, Cider1b1 + and Xspice. +""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = { + ('Bison', '3.0.2'), + ('flex', '2.5.39'), +} +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], + 'dirs': [], +} + + +moduleclass = 'lang' -- GitLab From 50debd2f2efd461b7970065d9fe5b68a19b69b1a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:10:50 +0200 Subject: [PATCH 0054/1172] set correct moduleclass --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 371953f64b..ca40da2a30 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -23,4 +23,4 @@ sanity_check_paths = { } -moduleclass = 'lang' +moduleclass = 'cae' -- GitLab From 38fc2d5668853b38041f8cc00d30cbca19efcddb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:12:41 +0200 Subject: [PATCH 0055/1172] remove whitespace --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index ca40da2a30..baa9131dc8 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -22,5 +22,4 @@ sanity_check_paths = { 'dirs': [], } - moduleclass = 'cae' -- GitLab From 381b0341849d633c556c066b9e83fabf8843fc02 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:43:10 +0200 Subject: [PATCH 0056/1172] be compatible with python 2.7.4 and lower --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index baa9131dc8..16f1a1e3ae 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -13,10 +13,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = { +dependencies = [ ('Bison', '3.0.2'), ('flex', '2.5.39'), -} +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], 'dirs': [], -- GitLab From f5e3d801b8d5854f755b21bd133cf92099e606af Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 9 Oct 2014 15:01:07 +0200 Subject: [PATCH 0057/1172] Pindel-0.2.5a7-goolf-1.4.10.eb --- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb new file mode 100644 index 0000000000..40569a3495 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.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 + +easyblock = 'CmdCp' + +name = 'Pindel' +version = '0.2.5a7' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized +insertions, inversions, tandem duplications and other structural variants at single-based +resolution from next-gen sequence data. It uses a pattern growth approach to identify the +breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('SAMtools', '0.1.19')] + +cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] + +files_to_copy = [(['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", "gmt", "gmt-web", "test", "README.md", "RELEASE" + ] + +postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c3c5b253a04ac10193c861fc7dcdbe8c6e2876cf Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 9 Oct 2014 17:29:23 +0200 Subject: [PATCH 0058/1172] indent description --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 40569a3495..f573781fab 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -10,9 +10,9 @@ version = '0.2.5a7' homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' description = """ Pindel can detect breakpoints of large deletions, medium sized -insertions, inversions, tandem duplications and other structural variants at single-based -resolution from next-gen sequence data. It uses a pattern growth approach to identify the -breakpoints of these variants from paired-end short reads. """ + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} -- GitLab From 20e02bdd6d8648674c7c5d06cb44882d318d3a10 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 13:59:19 +0100 Subject: [PATCH 0059/1172] bcftools-1.1-goolf-1.4.10.eb --- .../b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7cdafdabd6 --- /dev/null +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.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 + +name = 'bcftools' +version = '1.1' + +homepage = 'http://sourceforge.net/projects/samtools/' +description = """ utilities for variant calling and manipulating VCFs and BCFs """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bcftools", "plot-vcfstats", "vcfutils.pl"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 5a21cbf49efa11d287be4a3d9a9037936856e639 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:08:49 +0100 Subject: [PATCH 0060/1172] updated homepage --- easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb index 7cdafdabd6..f01baa3a62 100644 --- a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ name = 'bcftools' version = '1.1' -homepage = 'http://sourceforge.net/projects/samtools/' +homepage = 'http://www.htslib.org/' description = """ utilities for variant calling and manipulating VCFs and BCFs """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 0d6429b748258997e503a3d5bffcda38bd60ec88 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:12:10 +0100 Subject: [PATCH 0061/1172] updated description --- .../easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb index f01baa3a62..bbe68cc575 100644 --- a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb @@ -3,16 +3,17 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'bcftools' +name = 'BCFtools' version = '1.1' homepage = 'http://www.htslib.org/' -description = """ utilities for variant calling and manipulating VCFs and BCFs """ +description = """ Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising + SNP and short indel sequence variants """ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] -sources = [SOURCE_TAR_BZ2] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -- GitLab From 8df6608c234d23b05cc725a4284a6c646f224b42 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:12:34 +0100 Subject: [PATCH 0062/1172] renamed file --- ...{bcftools-1.1-goolf-1.4.10.eb => BCFtools-1.1-goolf-1.4.10.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/bcftools/{bcftools-1.1-goolf-1.4.10.eb => BCFtools-1.1-goolf-1.4.10.eb} (100%) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb -- GitLab From f6b67c22ae6a60e0c0a5114a1b192723c3fb97e2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:15:38 +0100 Subject: [PATCH 0063/1172] renamed dir --- .../b/{bcftools => BCFtools}/BCFtools-1.1-goolf-1.4.10.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/{bcftools => BCFtools}/BCFtools-1.1-goolf-1.4.10.eb (100%) diff --git a/easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb -- GitLab From e0646dbc44242889be7d7826b95f4e4a9d44fd04 Mon Sep 17 00:00:00 2001 From: Peter Maxwell Date: Tue, 28 Oct 2014 17:16:28 +1300 Subject: [PATCH 0064/1172] Easyconfigs for NCO and its dependency ANTLR --- .../a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 23 ++++++++++++++++++ .../a/ANTLR/ANTLR-cpp-headers.patch | 11 +++++++++ .../n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 24 +++++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb new file mode 100644 index 0000000000..029d2628ef --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -0,0 +1,23 @@ +name = "ANTLR" +version = "2.7.7" +homepage = "http://www.antlr2.org" +description = """ANother Tool for Language Recognition""" + +toolchain = {'version': '5.4.0', 'name': 'ictce'} + +assert version.startswith('2'), version +sources = ['antlr-%(version)s.tar.gz'] +source_urls = ['http://www.antlr2.org/download'] + +patches = ['ANTLR-cpp-headers.patch'] + +configopts = "--disable-examples --disable-csharp" + +dependencies = [('Java', '1.7.0_60', '', True)] + +sanity_check_paths = { + 'files': ['bin/antlr'], + 'dirs': ["."] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch b/easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch new file mode 100644 index 0000000000..e10f61e6d6 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch @@ -0,0 +1,11 @@ +--- antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2006-11-02 10:37:17.000000000 +1300 ++++ antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2014-08-25 13:06:46.541050000 +1200 +@@ -10,6 +10,8 @@ + + #include + ++#include ++#include + #include + + #ifdef HAS_NOT_CCTYPE_H diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb new file mode 100644 index 0000000000..9d934e4ab8 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -0,0 +1,24 @@ +name = "NCO" +version = '4.4.4' +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'version': '5.4.0', 'name': 'ictce'} + +sources = ['nco-%(version)s.tar.gz'] +source_urls = ['http://nco.sourceforge.net/src'] + +dependencies = [ + ('UDUNITS', '2.1.24'), + ('expat', '2.1.0'), + ('ANTLR', '2.7.7'), # incl C++ + ('GSL', '1.16'), + ('netCDF', '4.2'), +] + +sanity_check_paths = { + 'files': ['bin/ncap'], + 'dirs': ["."] +} + +moduleclass = 'tools' -- GitLab From b3c7cccab4a44af288db2fdf1b21afa94e35554e Mon Sep 17 00:00:00 2001 From: Peter Maxwell Date: Fri, 31 Oct 2014 12:45:22 +1300 Subject: [PATCH 0065/1172] ictce-5.4.0 versions of dependencies for NCO --- .../e/expat/expat-2.1.0-ictce-5.4.0.eb | 13 ++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb | 16 ++++++++ .../h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb | 25 +++++++++++ .../n/netCDF/netCDF-4.2-ictce-5.4.0.eb | 21 ++++++++++ .../s/Szip/Szip-2.1-ictce-5.4.0.eb | 20 +++++++++ .../u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb | 41 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-ictce-5.4.0.eb | 21 ++++++++++ 7 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb new file mode 100644 index 0000000000..35e3826b5e --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb @@ -0,0 +1,13 @@ +name = 'expat' +version = '2.1.0' + +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': 'ictce', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb new file mode 100644 index 0000000000..c8e5fe79ee --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb @@ -0,0 +1,16 @@ +name = 'GSL' +version = '1.16' + +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 = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb new file mode 100644 index 0000000000..4c1c1db157 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb @@ -0,0 +1,25 @@ +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': 'ictce', 'version': '5.4.0'} +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 = [ + 'HDF5_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb new file mode 100644 index 0000000000..a0f0b6f197 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +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': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +configopts = ['--disable-doxygen'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb new file mode 100644 index 0000000000..7a39513993 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb @@ -0,0 +1,20 @@ +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': 'ictce', 'version': '5.4.0'} +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.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb new file mode 100644 index 0000000000..1b81feb89b --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# 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 +## + +name = 'UDUNITS' +version = '2.1.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'opt': True, 'pic': True} + +# eg. ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +sanity_check_paths = { + 'files': [ + 'bin/udunits2', + 'include/converter.h', + 'include/udunits2.h', + 'include/udunits.h', + 'lib/libudunits2.a', + 'lib/libudunits2.so', + ], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb new file mode 100644 index 0000000000..938bf3da54 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb @@ -0,0 +1,21 @@ +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 = {'version': '5.4.0', 'name': 'ictce'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 887532fc2c252e8897c4e0ae52995fa190d0982b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 3 Nov 2014 09:37:22 +0100 Subject: [PATCH 0066/1172] 1 --- .../a/ATK/ATK-2.14.0-intel-2014b.eb | 30 +++++++++++++++ .../GDK-Pixbuf-2.30.7-intel-2014b.eb | 35 ++++++++++++++++++ ...Object-Introspection-1.42.0-intel-2014b.eb | 31 ++++++++++++++++ .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 33 +++++++++++++++++ .../p/Python/Python-2.7.8-intel-2014b.eb | 3 ++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 6 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb new file mode 100644 index 0000000000..24ac7dc408 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb @@ -0,0 +1,30 @@ +name = 'ATK' +version = '2.14.0' + +homepage = 'https://developer.gnome.org/atk/' +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': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), +] + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.so'], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb new file mode 100644 index 0000000000..cbcafc7f3f --- /dev/null +++ b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb @@ -0,0 +1,35 @@ +name = 'GDK-Pixbuf' +version = '2.30.7' + +homepage = 'https://developer.gnome.org/gdx-pixbuf/' +description = """GdkPixbuf is a library for image loading and manipulation. + The GdkPixbuf documentation contains both + the programmer's guide and the API reference.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('LibTIFF', '4.0.3'), +] + +configopts = '--with-x11 ' + +sanity_check_paths = { + 'files': ['bin/gdk-pixbuf-%s' % x for x in ['csource', 'pixdata', 'query-loaders']] + + ['lib/libgdk_pixbuf%s-2.0.so' % x for x in ['', '_xlib']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..a7d8444e44 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -0,0 +1,31 @@ +name = 'GObject-Introspection' +version = '1.42.0' + +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': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), +] + +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'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb new file mode 100644 index 0000000000..672e1ddf3e --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb @@ -0,0 +1,33 @@ +name = 'GTK+' +version = '2.24.25' + +homepage = 'http://www.gtk.org' +description = """GTK+, or the GIMP Toolkit, is a multi-platform toolkit + for creating graphical user interfaces. Offering a complete set of widgets, + GTK+ is suitable for projects ranging from small one-off tools + to complete application suites.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('Pango', '1.36.7'), + ('GObject-Introspection', '1.42.0'), + ('GDK-Pixbuf', '2.30.7'), + ('ATK', '2.14.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index fc03cf9418..76a6bcb647 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -90,6 +90,9 @@ exts_list = [ ('matplotlib', '1.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], }), + ('pyamg', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyamg/'], + }), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..e75705dfa5 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +name = 'wxPython' +version = '3.0.1.1' + +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': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +python = "Python" +pythonversion = '2.7.8' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libpng', '1.6.12'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.3.1'), + ('LibTIFF', '4.0.3'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 5ec7a8b7cf6b1356c442cb94c7289a8a935cbcbd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 5 Nov 2014 15:23:51 +0100 Subject: [PATCH 0067/1172] 2 --- .../b/Bison/Bison-2.5-intel-2014b.eb | 2 +- .../d/DBus/DBus-1.8.8-intel-2014b.eb | 22 ++++ .../dbus-glib/dbus-glib-0.102-intel-2014b.eb | 23 ++++ .../g/GConf/GConf-3.2.6-intel-2014b.eb | 34 ++++++ ...4b.eb => GDK-Pixbuf-2.30.8-intel-2014b.eb} | 2 +- .../GST-plugins-base-0.10.36-intel-2014b.eb | 32 ++++++ .../GStreamer-0.10.36-intel-2014b.eb | 36 ++++++ .../GStreamer/GStreamer-1.4.3-intel-2014b.eb | 38 ++++++ .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 7 +- .../i/intltool/intltool-0.50.2-intel-2014b.eb | 18 +++ .../l/libIDL/libIDL-0.8.14-intel-2014b.eb | 25 ++++ .../o/ORBit2/ORBit2-2.14.19-intel-2014b.eb | 25 ++++ .../o/ORBit2/ORBit2_2.14_fixgthread.patch | 24 ++++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 7 ++ .../w/wxPython/wxPython_3.0.1.1_intel.patch | 108 ++++++++++++++++++ 15 files changed, 398 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb rename easybuild/easyconfigs/g/GDK-Pixbuf/{GDK-Pixbuf-2.30.7-intel-2014b.eb => GDK-Pixbuf-2.30.8-intel-2014b.eb} (98%) create mode 100644 easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb create mode 100644 easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb create mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb create mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index d87f069c2c..e4774cf7c1 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.16')] +builddependencies = [('M4', '1.4.17')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb new file mode 100644 index 0000000000..63bfd61c8d --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb @@ -0,0 +1,22 @@ +name = 'DBus' +version = '1.8.8' + +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': '2014b'} + +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', 'so']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb new file mode 100644 index 0000000000..a67144380a --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb @@ -0,0 +1,23 @@ +name = 'dbus-glib' +version = '0.102' + +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': '2014b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('DBus', '1.8.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.so', 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb new file mode 100644 index 0000000000..d3feb03c97 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb @@ -0,0 +1,34 @@ +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', '0.102'), + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('ORBit2', '2.14.19'), + ('intltool', '0.50.2'), +] + +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/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb similarity index 98% rename from easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb rename to easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb index cbcafc7f3f..95ae4e8637 100644 --- a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb @@ -1,5 +1,5 @@ name = 'GDK-Pixbuf' -version = '2.30.7' +version = '2.30.8' homepage = 'https://developer.gnome.org/gdx-pixbuf/' description = """GdkPixbuf is a library for image loading and manipulation. diff --git a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb new file mode 100644 index 0000000000..cced46e20c --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb @@ -0,0 +1,32 @@ +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': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +builddependencies = [ + ('Bison', '2.5'), +] + +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-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb new file mode 100644 index 0000000000..f10f413e57 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb @@ -0,0 +1,36 @@ +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': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '2.5'), +] + +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/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb new file mode 100644 index 0000000000..3cefe8bf97 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb @@ -0,0 +1,38 @@ +name = 'GStreamer' +version = '1.4.3' + +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': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('M4', '1.4.17'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-1.0.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/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb index 672e1ddf3e..ab5dc7cedf 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb @@ -16,13 +16,14 @@ dependencies = [ ('GLib', '2.40.0'), ('Pango', '1.36.7'), ('GObject-Introspection', '1.42.0'), - ('GDK-Pixbuf', '2.30.7'), + ('GDK-Pixbuf', '2.30.8'), ('ATK', '2.14.0'), ] sanity_check_paths = { - 'files': [], - 'dirs': [] + 'files': ['bin/gtk-%s' % x for x in ['query-immodules-2.0', 'update-icon-cache', 'builder-convert', 'demo']] + + ['lib/libgailutil.so'] + ['lib/libg%sk-x11-2.0.so' % x for x in ['d','t']], + 'dirs': ['etc', 'include', 'share'] } modextrapaths = { diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb new file mode 100644 index 0000000000..a88c9eb891 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb @@ -0,0 +1,18 @@ +name = 'intltool' +version = '0.50.2' + +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': '2014b'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', 'ize', '-merge', '-prepare', '-update']], + 'dirs': ['share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb new file mode 100644 index 0000000000..be7a93b01a --- /dev/null +++ b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb @@ -0,0 +1,25 @@ +name = 'libIDL' +version = '0.8.14' + +homepage = 'http://freecode.com/projects/libidl' +description = """libIDL is a library for creating trees of CORBA Interface Definition Language (IDL) + files, which is a specification for defining portable interfaces. libIDL was + initially written for ORBit (the ORB from the GNOME project, and the primaryi + means of libIDL distribution). However, the functionalityi + was designed to be as reusable and portable as possible.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/libIDL/%(version_major_minor)s'] +sources = [SOURCE_TAR_BZ2] + +dependencies = [ + ('GLib', '2.40.0'), +] + +sanity_check_paths = { + 'files': ['bin/libIDL-config-2', 'lib/libIDL-2.a', 'lib/libIDL-2.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb new file mode 100644 index 0000000000..bfbf9c366f --- /dev/null +++ b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb @@ -0,0 +1,25 @@ +name = 'ORBit2' +version = '2.14.19' + +homepage = 'https://projects.gnome.org/ORBit2/' +description = """ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/ORBit2/%(version_major_minor)s'] +sources = [SOURCE_TAR_GZ] + +patches = ['ORBit2_%(version_major_minor)s_fixgthread.patch'] + +dependencies = [ + ('GLib', '2.40.0'), + ('libIDL', '0.8.14') +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ior-decode-2', 'linc-cleanup-sockets', 'orbit2-config', 'orbit-idl-2', 'typelib-dump']] + + ['lib/lib%s.%s' % (x,y) for x in ['ORBit-2', 'ORBitCosNaming-2', 'ORBit-imodule-2'] for y in ['a', 'so']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch new file mode 100644 index 0000000000..5d793515cd --- /dev/null +++ b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch @@ -0,0 +1,24 @@ +# http://stackoverflow.com/questions/25590498/cannot-build-orbit2-fix-apparently-found-but-where-is-it +--- ORBit2-2.14.19.ORIG/linc2/src/Makefile.am 2010-02-09 13:05:35.000000000 +0100 ++++ ORBit2-2.14.19/linc2/src/Makefile.am 2014-11-03 16:58:20.518982441 +0100 +@@ -12,8 +12,7 @@ + -I$(top_builddir)/linc2/include \ + -I$(top_srcdir)/linc2/include \ + $(LINC_CFLAGS) \ +- $(WARN_CFLAGS) \ +- -DG_DISABLE_DEPRECATED ++ $(WARN_CFLAGS) + + if OS_WIN32 + else +--- ORBit2-2.14.19.ORIG/linc2/src/Makefile.in 2010-09-28 11:39:39.000000000 +0200 ++++ ORBit2-2.14.19/linc2/src/Makefile.in 2014-11-04 09:20:14.000518250 +0100 +@@ -244,7 +244,7 @@ + # -I$(top_srcdir)/include + INCLUDES = -I$(top_builddir)/linc2/include \ + -I$(top_srcdir)/linc2/include $(LINC_CFLAGS) $(WARN_CFLAGS) \ +- -DG_DISABLE_DEPRECATED $(am__append_1) ++ $(am__append_1) + liblinc_la_SOURCES = \ + linc.c \ + linc-connection.c \ diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb index e75705dfa5..00aefd6867 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tar.bz2'] +patches = ['%(name)s_%(version)s_intel.patch'] + python = "Python" pythonversion = '2.7.8' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) @@ -27,8 +29,13 @@ dependencies = [ ('libjpeg-turbo', '1.3.1'), ('LibTIFF', '4.0.3'), ('expat', '2.1.0'), + ('GTK+', '2.24.25'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), ] +parallel = 1 + sanity_check_paths = { 'files': [], 'dirs': [] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch new file mode 100644 index 0000000000..a69e52d13a --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch @@ -0,0 +1,108 @@ +# PATCH for intel compiler +# see http://trac.wxwidgets.org/ticket/15267 +# second part inspired by ---^ +# B. Hajgato Nov 04 2014 +--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 ++++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:05:58.460396471 +0100 +@@ -16977,7 +16977,7 @@ + $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + monodll_extended.o: $(srcdir)/src/common/extended.c $(MONODLL_ODEP) +- $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c + + monodll_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONODLL_ODEP) + $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -22851,7 +22851,7 @@ + $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + monolib_extended.o: $(srcdir)/src/common/extended.c $(MONOLIB_ODEP) +- $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c + + monolib_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONOLIB_ODEP) + $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -28725,7 +28725,7 @@ + $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + basedll_extended.o: $(srcdir)/src/common/extended.c $(BASEDLL_ODEP) +- $(CCC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c + + basedll_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASEDLL_ODEP) + $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -29241,7 +29241,7 @@ + $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + baselib_extended.o: $(srcdir)/src/common/extended.c $(BASELIB_ODEP) +- $(CCC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c + + baselib_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASELIB_ODEP) + $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +#--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 +#+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:25:41.507128586 +0100 +#@@ -22653,13 +22653,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONODLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONODLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONODLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONODLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -28527,13 +28527,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONOLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONOLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONOLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONOLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -38955,13 +38955,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVDLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVDLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVDLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVDLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -39426,13 +39426,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -- GitLab From b26c3aaa4fa20e86f329b08ab27162a7dc34cacc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 5 Nov 2014 15:43:05 +0100 Subject: [PATCH 0068/1172] ncdf4 - netcdf4 for R 3.1.1 intel2014b --- .../n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000..cdf98f1940 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.13' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2') +] + +moduleclass = 'math' -- GitLab From 98a44a2ff6ac5530414bd183076d2ab7d42a85a0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 7 Nov 2014 16:57:34 +0000 Subject: [PATCH 0069/1172] Just bumping the bowtie version to the most recent. Compiles fine under goolf 1.4.10 Adding an author name so that users can complain more directly --- .../b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..0240ff0e2c --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team + +name = 'Bowtie' +version = '1.1.1' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From fd60f5e07dc37691e637385e979077bbe211746c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Nov 2014 10:58:52 +0100 Subject: [PATCH 0070/1172] 3 --- .../w/wxPython/wxPython_3.0.1.1_intel.patch | 120 ++---------------- 1 file changed, 12 insertions(+), 108 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch index a69e52d13a..f91d3210f4 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch @@ -1,108 +1,12 @@ -# PATCH for intel compiler -# see http://trac.wxwidgets.org/ticket/15267 -# second part inspired by ---^ -# B. Hajgato Nov 04 2014 ---- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 -+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:05:58.460396471 +0100 -@@ -16977,7 +16977,7 @@ - $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - monodll_extended.o: $(srcdir)/src/common/extended.c $(MONODLL_ODEP) -- $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c - - monodll_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONODLL_ODEP) - $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -22851,7 +22851,7 @@ - $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - monolib_extended.o: $(srcdir)/src/common/extended.c $(MONOLIB_ODEP) -- $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c - - monolib_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONOLIB_ODEP) - $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -28725,7 +28725,7 @@ - $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - basedll_extended.o: $(srcdir)/src/common/extended.c $(BASEDLL_ODEP) -- $(CCC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c - - basedll_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASEDLL_ODEP) - $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -29241,7 +29241,7 @@ - $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - baselib_extended.o: $(srcdir)/src/common/extended.c $(BASELIB_ODEP) -- $(CCC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c - - baselib_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASELIB_ODEP) - $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -#--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 -#+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:25:41.507128586 +0100 -#@@ -22653,13 +22653,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONODLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONODLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONODLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONODLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -28527,13 +28527,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONOLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONOLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONOLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONOLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -38955,13 +38955,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVDLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVDLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVDLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVDLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -39426,13 +39426,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) +# B. Hajgato Nov 07 2014 +--- wxPython-src-3.0.1.1.ORIG/build/tools/build-wxwidgets.py 2014-01-04 22:08:37.000000000 +0100 ++++ wxPython-src-3.0.1.1/build/tools/build-wxwidgets.py 2014-11-07 14:02:02.144031589 +0100 +@@ -265,6 +265,7 @@ + configure_opts.append("--with-osx_cocoa") + + wxpy_configure_opts = [ ++ "--disable-precomp-headers", + "--with-opengl", + "--enable-sound", + "--enable-graphics_ctx", -- GitLab From 6ce40a54a62e04bdd6dd4a10f9c4fdfef3672440 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 11:05:49 +0100 Subject: [PATCH 0071/1172] Update to NWChem 6.5 --- ...243-intel-2014b-2014-09-10-Python-2.7.8.eb | 31 +++++++++++++++++++ ...Chem-6.5.revision26243-parallelbuild.patch | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb new file mode 100644 index 0000000000..2eefc9a7f3 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -0,0 +1,31 @@ +name = 'NWChem' +version = '6.5.revision26243' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'i8': True} + +source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +verdate = '2014-09-10' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch new file mode 100644 index 0000000000..8558fe4778 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -0,0 +1,29 @@ +--- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 ++++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1394,7 +1394,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1814,7 +1814,7 @@ + endif + endif + DEFINES += -DEXT_INT +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + _CPU = $(shell uname -m ) + ifeq ($(BLAS_LIB),) + CORE_SUBDIRS_EXTRA += blas +@@ -1923,7 +1923,7 @@ + endif # end of ia32 bit + ifeq ($(_CPU),x86_64) + # +- MAKEFLAGS = -j 2 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + COPTIMIZE = -O1 + ifeq ($(NWCHEM_TARGET),CATAMOUNT) + FC=pgf90 -- GitLab From 3e0d9181f1d2410c61038d17e962c9f5a1adb896 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Nov 2014 13:37:49 +0100 Subject: [PATCH 0072/1172] minor style fixes --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 4 ++-- easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb | 2 +- easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 6 +++--- easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb | 1 + .../easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb | 1 + 6 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index 029d2628ef..898817073d 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -1,11 +1,11 @@ name = "ANTLR" version = "2.7.7" + homepage = "http://www.antlr2.org" description = """ANother Tool for Language Recognition""" -toolchain = {'version': '5.4.0', 'name': 'ictce'} +toolchain = {'name': 'ictce', 'version': '5.4.0'} -assert version.startswith('2'), version sources = ['antlr-%(version)s.tar.gz'] source_urls = ['http://www.antlr2.org/download'] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb index 35e3826b5e..baf28602a2 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb @@ -4,10 +4,10 @@ version = '2.1.0' 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': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb index 9d934e4ab8..894db7ff0c 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -3,15 +3,15 @@ version = '4.4.4' homepage = "http://nco.sourceforge.net" description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" -toolchain = {'version': '5.4.0', 'name': 'ictce'} +toolchain = {'name': 'ictce', 'version': '5.4.0'} -sources = ['nco-%(version)s.tar.gz'] source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('UDUNITS', '2.1.24'), ('expat', '2.1.0'), - ('ANTLR', '2.7.7'), # incl C++ + ('ANTLR', '2.7.7'), ('GSL', '1.16'), ('netCDF', '4.2'), ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb index 7a39513993..43f9f7b55c 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb @@ -3,6 +3,7 @@ version = '2.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" + toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb index 1b81feb89b..c235471294 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb @@ -20,7 +20,6 @@ description = """UDUNITS supports conversion of unit specifications between form toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'opt': True, 'pic': True} -# eg. ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb index 938bf3da54..931cdbbadb 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb @@ -5,6 +5,7 @@ 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 = {'version': '5.4.0', 'name': 'ictce'} toolchainopts = {'optarch': True, 'pic': True} -- GitLab From be2e1a846780b2e72fa1884f695d734ab35a4950 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Nov 2014 13:40:47 +0100 Subject: [PATCH 0073/1172] rename ANTLR patch to include version --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../{ANTLR-cpp-headers.patch => ANTLR-2.7.7_cpp-headers.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/ANTLR/{ANTLR-cpp-headers.patch => ANTLR-2.7.7_cpp-headers.patch} (100%) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index 898817073d..c65bc28385 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = ['antlr-%(version)s.tar.gz'] source_urls = ['http://www.antlr2.org/download'] -patches = ['ANTLR-cpp-headers.patch'] +patches = ['ANTLR-%(version)s_cpp-headers.patch'] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch similarity index 100% rename from easybuild/easyconfigs/a/ANTLR/ANTLR-cpp-headers.patch rename to easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch -- GitLab From bcf59593203e63bbcd540e3995a78762d315f363 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Nov 2014 13:47:53 +0100 Subject: [PATCH 0074/1172] add easyconfigs for NCO/ANTLR with intel/2014b toolchain --- .../a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 23 +++++++++++ .../e/expat/expat-2.1.0-intel-2014b.eb | 13 ++++++ .../h/HDF5/HDF5-1.8.9-intel-2014b.eb | 25 ++++++++++++ .../n/NCO/NCO-4.4.4-intel-2014b.eb | 24 +++++++++++ .../n/netCDF/netCDF-4.2-intel-2014b.eb | 21 ++++++++++ .../u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb | 40 +++++++++++++++++++ 6 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb new file mode 100644 index 0000000000..4d1d684632 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -0,0 +1,23 @@ +name = "ANTLR" +version = "2.7.7" + +homepage = "http://www.antlr2.org" +description = """ANother Tool for Language Recognition""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['antlr-%(version)s.tar.gz'] +source_urls = ['http://www.antlr2.org/download'] + +patches = ['ANTLR-cpp-headers.patch'] + +configopts = "--disable-examples --disable-csharp" + +dependencies = [('Java', '1.7.0_60', '', True)] + +sanity_check_paths = { + 'files': ['bin/antlr'], + 'dirs': ["."] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb new file mode 100644 index 0000000000..fee1afb9ea --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb @@ -0,0 +1,13 @@ +name = 'expat' +version = '2.1.0' + +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': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb new file mode 100644 index 0000000000..24af13ad70 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb @@ -0,0 +1,25 @@ +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': 'intel', 'version': '2014b'} +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 = [ + 'HDF5_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb new file mode 100644 index 0000000000..836532644c --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -0,0 +1,24 @@ +name = "NCO" +version = '4.4.4' +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('UDUNITS', '2.1.24'), + ('expat', '2.1.0'), + ('ANTLR', '2.7.7'), + ('GSL', '1.16'), + ('netCDF', '4.2'), +] + +sanity_check_paths = { + 'files': ['bin/ncap'], + 'dirs': ["."] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb new file mode 100644 index 0000000000..fc24bdb27f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +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': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +configopts = ['--disable-doxygen'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb new file mode 100644 index 0000000000..161a232d35 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# 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 +## + +name = 'UDUNITS' +version = '2.1.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +sanity_check_paths = { + 'files': [ + 'bin/udunits2', + 'include/converter.h', + 'include/udunits2.h', + 'include/udunits.h', + 'lib/libudunits2.a', + 'lib/libudunits2.so', + ], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From 383b9bb419098a60a49920cbda0dfda0e347a291 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Nov 2014 14:12:39 +0100 Subject: [PATCH 0075/1172] fix NCO sanity check --- easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb index 836532644c..0437447001 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -17,8 +17,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/ncap'], - 'dirs': ["."] + 'files': ['bin/nc%s' % x for x in ['ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', + 'ks', 'pdq', 'ra', 'rcat', 'rename']] + + ['lib/libnco.a', 'lib/libnco.so', 'lib/libnco_c++.a', 'lib/libnco_c++.so'], + 'dirs': ['include'], } moduleclass = 'tools' -- GitLab From a8d699b11c25fa0f9eef01317e97c076653ef451 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 16:43:53 +0100 Subject: [PATCH 0076/1172] No vec-report, please --- ...Chem-6.5.revision26243-parallelbuild.patch | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch index 8558fe4778..c3a7a32982 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -1,5 +1,16 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 --- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 +++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1231,7 +1231,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif @@ -1394,7 +1394,7 @@ CORE_SUBDIRS_EXTRA = blas lapack CC = gcc @@ -9,6 +20,24 @@ INSTALL = @echo $@ is built CPP = gcc -E -nostdinc -undef -P FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1527,7 +1527,7 @@ + DEFINES += -DGFORTRAN + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1602,7 +1602,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII @@ -1814,7 +1814,7 @@ endif endif @@ -27,3 +56,37 @@ COPTIMIZE = -O1 ifeq ($(NWCHEM_TARGET),CATAMOUNT) FC=pgf90 +@@ -1959,19 +1959,17 @@ + ifeq ($(_IFCV15ORNEWER), Y) + FOPTIONS += -qopt-report-file=stderr + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -2086,9 +2084,9 @@ + ICCV15ORNEWER=$(shell icc -V 2>&1|egrep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}') + COPTIONS += -xHOST -ftz + ifeq ($(ICCV15ORNEWER), Y) +- COPTIONS += -qopt-report-phase:openmp -vec-report=1 ++ COPTIONS += -qopt-report-phase:openmp + else +- COPTIONS += -openmp-report=2 -vec-report=1 ++ COPTIONS += -openmp-report0 + endif + #old COPTIMIZE = -O3 -hlo -mP2OPT_hlo_level=2 + COPTIMIZE = -O3 -- GitLab From f4b5ba20ab0cb36b7c5e1f72a33c08e6a2277454 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Nov 2014 10:47:04 +0100 Subject: [PATCH 0077/1172] bump NCO dep netCDF version for compatibility reasons --- easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb index 0437447001..c79a55883a 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -13,7 +13,7 @@ dependencies = [ ('expat', '2.1.0'), ('ANTLR', '2.7.7'), ('GSL', '1.16'), - ('netCDF', '4.2'), + ('netCDF', '4.2.1.1'), ] sanity_check_paths = { -- GitLab From 554b575574dada85f4420eae9448291378ea63dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Nov 2014 10:52:31 +0100 Subject: [PATCH 0078/1172] bump netCDF version as dep for NCO to latest v4.2.x + add missing easyconfigs --- .../b/Bison/Bison-2.7-ictce-5.4.0.eb | 20 ++++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb | 18 +++++++++++++ .../f/flex/flex-2.5.37-ictce-5.4.0.eb | 14 ++++++++++ .../h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb | 27 +++++++++++++++++++ .../n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 2 +- .../n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb | 19 +++++++++++++ .../z/zlib/zlib-1.2.7-ictce-5.4.0.eb | 20 ++++++++++++++ 7 files changed, 119 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb new file mode 100644 index 0000000000..155ffc59c6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '2.7' + +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': '5.4.0'} + +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/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb new file mode 100644 index 0000000000..76e4e4d410 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': '5.4.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb new file mode 100644 index 0000000000..bf5ece9d3c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb new file mode 100644 index 0000000000..126e473584 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '5.4.0'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb index 894db7ff0c..c9311e3b3b 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('expat', '2.1.0'), ('ANTLR', '2.7.7'), ('GSL', '1.16'), - ('netCDF', '4.2'), + ('netCDF', '4.2.1.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb new file mode 100644 index 0000000000..49f253f65d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +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': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb new file mode 100644 index 0000000000..6252bc5bba --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb @@ -0,0 +1,20 @@ +name = 'zlib' +version = '1.2.7' + +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': 'ictce', 'version': '5.4.0'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 052255acda56971ab3ef7580b2f53e3cab11cad3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Nov 2014 10:53:52 +0100 Subject: [PATCH 0079/1172] fix patch name in ANTLR easyconfig --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 4d1d684632..6d47d1483d 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = ['antlr-%(version)s.tar.gz'] source_urls = ['http://www.antlr2.org/download'] -patches = ['ANTLR-cpp-headers.patch'] +patches = ['ANTLR-%(version)s_cpp-headers.patch'] configopts = "--disable-examples --disable-csharp" -- GitLab From 9aafec03d3092d979d73f1d276e14adb2319db2a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 19 Nov 2014 16:05:29 +0100 Subject: [PATCH 0080/1172] HTSeq for intel-2014b plus version bump --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..1f11e79748 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' -- GitLab From c0bb88458cd4a7001b66d7cddb4459b98f5bff8e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 28 Nov 2014 14:30:34 +0100 Subject: [PATCH 0081/1172] 3 --- ...rcuitscape-4.0-intel-2014b-Python-2.7.8.eb | 35 +++++++++++++++++++ ...thonCard-0.8.2-intel-2014b-Python-2.7.8.eb | 31 ++++++++++++++++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 10 ++++-- 3 files changed, 74 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..1285fae586 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'Circuitscape' +version = '4.0.5' + +homepage = 'http://www.circuitscape.org/' +description = """Circuitscape is a free, open-source program which borrows algorithms + from electronic circuit theory to predict patterns of movement, gene flow, + and genetic differentiation among plant and animal populations in + heterogeneous landscapes. Circuit theory complements least-cost path + approaches because it considers effects of all possible pathways + across a landscape simultaneously.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('PythonCard', '0.8.2', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(namelower)s/__init__.py' % pyshortver] + + ['bin/cs%s.py' % x for x in ['run', 'verify']], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..4343c60c4e --- /dev/null +++ b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PythonCard' +version = '0.8.2' + +homepage = 'http://pythoncard.sourceforge.net/' +description = """PythonCard is a GUI construction kit for building cross-platform desktop + applications on Windows, Mac OS X, and Linux, using the Python language.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('wxPython', '3.0.1.1', versionsuffix), +] +exts_filter = ('python -c "import PythonCard"', "") + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%s/__init__.py' % (pyshortver,name)], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver,name)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb index 00aefd6867..c4c88fa0d8 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -37,8 +37,14 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': [], - 'dirs': [] + '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%s/site-packages' % pythonshortversion ] +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages/wx-3.0-gtk2' % pythonshortversion ], } moduleclass = 'vis' -- GitLab From 6f7529dc84bb7a7dc452d75b5bbba05eb5dfd330 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Dec 2014 09:20:44 +0100 Subject: [PATCH 0082/1172] Circuitscape4 --- .../a/ATK/ATK-2.14.0-intel-2014b.eb | 30 ----------- .../b/Bison/Bison-2.5-intel-2014b.eb | 2 +- ...itscape-4.0.5-intel-2014b-Python-2.7.8.eb} | 1 - .../d/DBus/DBus-1.8.8-intel-2014b.eb | 22 -------- .../dbus-glib/dbus-glib-0.102-intel-2014b.eb | 23 --------- .../g/GConf/GConf-3.2.6-intel-2014b.eb | 34 ------------- .../GDK-Pixbuf-2.30.8-intel-2014b.eb | 35 ------------- ...Object-Introspection-1.42.0-intel-2014b.eb | 31 ------------ .../GST-plugins-base-0.10.36-intel-2014b.eb | 32 ------------ .../GStreamer-0.10.36-intel-2014b.eb | 36 ------------- .../GStreamer/GStreamer-1.4.3-intel-2014b.eb | 38 -------------- .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 34 ------------- .../i/intltool/intltool-0.50.2-intel-2014b.eb | 18 ------- .../l/libIDL/libIDL-0.8.14-intel-2014b.eb | 25 ---------- .../o/ORBit2/ORBit2-2.14.19-intel-2014b.eb | 25 ---------- .../o/ORBit2/ORBit2_2.14_fixgthread.patch | 24 --------- ...thonCard-0.8.2-intel-2014b-Python-2.7.8.eb | 31 ------------ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 50 ------------------- .../w/wxPython/wxPython_3.0.1.1_intel.patch | 12 ----- 19 files changed, 1 insertion(+), 502 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb rename easybuild/easyconfigs/c/Circuitscape/{Circuitscape-4.0-intel-2014b-Python-2.7.8.eb => Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb} (96%) delete mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch delete mode 100644 easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb deleted file mode 100644 index 24ac7dc408..0000000000 --- a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'ATK' -version = '2.14.0' - -homepage = 'https://developer.gnome.org/atk/' -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': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), -] - -sanity_check_paths = { - 'files': ['lib/libatk-1.0.so'], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index e4774cf7c1..d87f069c2c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17')] +builddependencies = [('M4', '1.4.16')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb similarity index 96% rename from easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb index 1285fae586..a07b1584dc 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -23,7 +23,6 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), - ('PythonCard', '0.8.2', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb deleted file mode 100644 index 63bfd61c8d..0000000000 --- a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'DBus' -version = '1.8.8' - -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': '2014b'} - -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', 'so']], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb deleted file mode 100644 index a67144380a..0000000000 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'dbus-glib' -version = '0.102' - -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': '2014b'} - -source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('DBus', '1.8.8'), - ('expat', '2.1.0'), -] - -sanity_check_paths = { - 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.so', 'lib/libdbus-glib-1.a'], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb deleted file mode 100644 index d3feb03c97..0000000000 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb +++ /dev/null @@ -1,34 +0,0 @@ -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', '0.102'), - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('ORBit2', '2.14.19'), - ('intltool', '0.50.2'), -] - -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/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb deleted file mode 100644 index 95ae4e8637..0000000000 --- a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'GDK-Pixbuf' -version = '2.30.8' - -homepage = 'https://developer.gnome.org/gdx-pixbuf/' -description = """GdkPixbuf is a library for image loading and manipulation. - The GdkPixbuf documentation contains both - the programmer's guide and the API reference.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('libjpeg-turbo', '1.3.1'), - ('libpng', '1.6.12'), - ('LibTIFF', '4.0.3'), -] - -configopts = '--with-x11 ' - -sanity_check_paths = { - 'files': ['bin/gdk-pixbuf-%s' % x for x in ['csource', 'pixdata', 'query-loaders']] + - ['lib/libgdk_pixbuf%s-2.0.so' % x for x in ['', '_xlib']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' 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 deleted file mode 100644 index a7d8444e44..0000000000 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'GObject-Introspection' -version = '1.42.0' - -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': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), -] - -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'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb deleted file mode 100644 index cced46e20c..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb +++ /dev/null @@ -1,32 +0,0 @@ -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': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [('GStreamer', '0.10.36')] - -builddependencies = [ - ('Bison', '2.5'), -] - -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-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb deleted file mode 100644 index f10f413e57..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb +++ /dev/null @@ -1,36 +0,0 @@ -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': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('zlib', '1.2.8'), -] - -builddependencies = [ - ('Bison', '2.5'), -] - -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/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb deleted file mode 100644 index 3cefe8bf97..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'GStreamer' -version = '1.4.3' - -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': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('zlib', '1.2.8'), -] - -builddependencies = [ - ('Bison', '3.0.2'), - ('flex', '2.5.39'), - ('M4', '1.4.17'), -] - -sanity_check_paths = { - 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-1.0.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/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb deleted file mode 100644 index ab5dc7cedf..0000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'GTK+' -version = '2.24.25' - -homepage = 'http://www.gtk.org' -description = """GTK+, or the GIMP Toolkit, is a multi-platform toolkit - for creating graphical user interfaces. Offering a complete set of widgets, - GTK+ is suitable for projects ranging from small one-off tools - to complete application suites.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('Pango', '1.36.7'), - ('GObject-Introspection', '1.42.0'), - ('GDK-Pixbuf', '2.30.8'), - ('ATK', '2.14.0'), -] - -sanity_check_paths = { - 'files': ['bin/gtk-%s' % x for x in ['query-immodules-2.0', 'update-icon-cache', 'builder-convert', 'demo']] + - ['lib/libgailutil.so'] + ['lib/libg%sk-x11-2.0.so' % x for x in ['d','t']], - 'dirs': ['etc', 'include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb deleted file mode 100644 index a88c9eb891..0000000000 --- a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'intltool' -version = '0.50.2' - -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': '2014b'} - -source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/intltool%s' % x for x in ['-extract', 'ize', '-merge', '-prepare', '-update']], - 'dirs': ['share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb deleted file mode 100644 index be7a93b01a..0000000000 --- a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'libIDL' -version = '0.8.14' - -homepage = 'http://freecode.com/projects/libidl' -description = """libIDL is a library for creating trees of CORBA Interface Definition Language (IDL) - files, which is a specification for defining portable interfaces. libIDL was - initially written for ORBit (the ORB from the GNOME project, and the primaryi - means of libIDL distribution). However, the functionalityi - was designed to be as reusable and portable as possible.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/libIDL/%(version_major_minor)s'] -sources = [SOURCE_TAR_BZ2] - -dependencies = [ - ('GLib', '2.40.0'), -] - -sanity_check_paths = { - 'files': ['bin/libIDL-config-2', 'lib/libIDL-2.a', 'lib/libIDL-2.so'], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb deleted file mode 100644 index bfbf9c366f..0000000000 --- a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'ORBit2' -version = '2.14.19' - -homepage = 'https://projects.gnome.org/ORBit2/' -description = """ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/ORBit2/%(version_major_minor)s'] -sources = [SOURCE_TAR_GZ] - -patches = ['ORBit2_%(version_major_minor)s_fixgthread.patch'] - -dependencies = [ - ('GLib', '2.40.0'), - ('libIDL', '0.8.14') -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ior-decode-2', 'linc-cleanup-sockets', 'orbit2-config', 'orbit-idl-2', 'typelib-dump']] + - ['lib/lib%s.%s' % (x,y) for x in ['ORBit-2', 'ORBitCosNaming-2', 'ORBit-imodule-2'] for y in ['a', 'so']], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch deleted file mode 100644 index 5d793515cd..0000000000 --- a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch +++ /dev/null @@ -1,24 +0,0 @@ -# http://stackoverflow.com/questions/25590498/cannot-build-orbit2-fix-apparently-found-but-where-is-it ---- ORBit2-2.14.19.ORIG/linc2/src/Makefile.am 2010-02-09 13:05:35.000000000 +0100 -+++ ORBit2-2.14.19/linc2/src/Makefile.am 2014-11-03 16:58:20.518982441 +0100 -@@ -12,8 +12,7 @@ - -I$(top_builddir)/linc2/include \ - -I$(top_srcdir)/linc2/include \ - $(LINC_CFLAGS) \ -- $(WARN_CFLAGS) \ -- -DG_DISABLE_DEPRECATED -+ $(WARN_CFLAGS) - - if OS_WIN32 - else ---- ORBit2-2.14.19.ORIG/linc2/src/Makefile.in 2010-09-28 11:39:39.000000000 +0200 -+++ ORBit2-2.14.19/linc2/src/Makefile.in 2014-11-04 09:20:14.000518250 +0100 -@@ -244,7 +244,7 @@ - # -I$(top_srcdir)/include - INCLUDES = -I$(top_builddir)/linc2/include \ - -I$(top_srcdir)/linc2/include $(LINC_CFLAGS) $(WARN_CFLAGS) \ -- -DG_DISABLE_DEPRECATED $(am__append_1) -+ $(am__append_1) - liblinc_la_SOURCES = \ - linc.c \ - linc-connection.c \ diff --git a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb deleted file mode 100644 index 4343c60c4e..0000000000 --- a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'PythonCard' -version = '0.8.2' - -homepage = 'http://pythoncard.sourceforge.net/' -description = """PythonCard is a GUI construction kit for building cross-platform desktop - applications on Windows, Mac OS X, and Linux, using the Python language.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pythonver = '2.7.8' -pyshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) - -dependencies = [ - (python, pythonver), - ('wxPython', '3.0.1.1', versionsuffix), -] -exts_filter = ('python -c "import PythonCard"', "") - -sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%s/__init__.py' % (pyshortver,name)], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver,name)], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb deleted file mode 100644 index c4c88fa0d8..0000000000 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ /dev/null @@ -1,50 +0,0 @@ -name = 'wxPython' -version = '3.0.1.1' - -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': '2014b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s-src-%(version)s.tar.bz2'] - -patches = ['%(name)s_%(version)s_intel.patch'] - -python = "Python" -pythonversion = '2.7.8' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), - ('libpng', '1.6.12'), - ('zlib', '1.2.8'), - ('libjpeg-turbo', '1.3.1'), - ('LibTIFF', '4.0.3'), - ('expat', '2.1.0'), - ('GTK+', '2.24.25'), - ('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%s/site-packages' % pythonshortversion ] -} - -modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages/wx-3.0-gtk2' % pythonshortversion ], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch deleted file mode 100644 index f91d3210f4..0000000000 --- a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) -# B. Hajgato Nov 07 2014 ---- wxPython-src-3.0.1.1.ORIG/build/tools/build-wxwidgets.py 2014-01-04 22:08:37.000000000 +0100 -+++ wxPython-src-3.0.1.1/build/tools/build-wxwidgets.py 2014-11-07 14:02:02.144031589 +0100 -@@ -265,6 +265,7 @@ - configure_opts.append("--with-osx_cocoa") - - wxpy_configure_opts = [ -+ "--disable-precomp-headers", - "--with-opengl", - "--enable-sound", - "--enable-graphics_ctx", -- GitLab From b85d1c25f711fd686a68e0b949c4ddc96a3ab93e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:03:42 +0100 Subject: [PATCH 0083/1172] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index ca812f75ef..facf14e7e4 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,7 +15,10 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5") +] options = {'modulename': 'DBD::Pg'} -- GitLab From 4d7b48d4445c3f6bdfe814b192939a7ea471c927 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:28 +0100 Subject: [PATCH 0084/1172] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 9b40199a4f..33c2f00038 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,7 +16,10 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [ + ('openssl-devel', + 'libssl-dev') +] java = 'Java' javaver = '1.7.0_60' @@ -25,6 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From cbf893e6a96a5c2c5e5031fe46e3e1f857ff221f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:47 +0100 Subject: [PATCH 0085/1172] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 33c2f00038..0adb8caf54 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -28,7 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From 60481d2dbba84675f5352ce5129dfc6319e19d7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:09:08 +0100 Subject: [PATCH 0086/1172] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 0adb8caf54..b5c98f2a72 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,10 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [ - ('openssl-devel', - 'libssl-dev') -] +osdependencies = [('openssl-devel', 'libssl-dev')] java = 'Java' javaver = '1.7.0_60' -- GitLab From 0af857faf426e0f6df19ce44fb0adb7710022a39 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 11 Dec 2014 18:08:51 +0100 Subject: [PATCH 0087/1172] MACS easyconfig --- .../MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..9912401ae1 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,69 @@ +# Built with EasyBuild version 1.15.2 on 2014-12-11_18-03-37 +# 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 + +easyblock = "PythonPackage" + +name = 'MACS' +version = '1.4.2-1' + +homepage = 'http://liulab.dfci.harvard.edu/MACS/' +description = """ Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers + such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of + the sequenced ChIP fragments, which tends to be shorter than sonication or library + construction size estimates, and uses it to improve the spatial resolution of predicted + binding sites. MACS also uses a dynamic Poisson distribution to effectively capture + local biases in the genome sequence, allowing for more sensitive and robust prediction.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/downloads/taoliu/MACS/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +options = {'modulename': 'MACS14'} + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/macs14'], + 'dirs': [''], +} + +moduleclass = 'bio' + + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "1.15.2", + "easybuild-easyblocks_version": "1.15.2", + "timestamp": 1418317417, + "build_time": 55.91, + "install_size": 412887, + "command_line": ['--buildpath=/tmp/easybuild', '--installpath=/import/bc2', '--modules-tool=Lmod', '--repositorypath=/import/bc2/soft/centos6/installation_recipes/installed_easyconfigs_sandybridge', '--sourcepath=/import/bc2/soft/source', '--subdir-software=apps', 'MACS-1.4.2-1-goolf-1.4.10.eb'], + "modules_tool": ('Lmod', '/import/bc2/soft/system/apps/lmod/lmod/libexec/lmod', '5.7.4'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2601.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/import/bc2/apps/GCC/4.7.2/libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran,lto --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=/import/bc2/apps/GCC/4.7.2 --with-local-prefix=/import/bc2/apps/GCC/4.7.2; Thread model: posix; gcc version 4.7.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "login11", + "kernel_name": "Linux", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.5", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 22 2013, 12:16:22) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/import/bc2/apps/GCC/4.7.2/bin/gcc", + "system_python_path": "/import/bc2/apps/Python/2.7.5-goolf-1.4.10/bin/python", +}] -- GitLab From 67acfc3b1072a7c009c3b83d037cfd899ef3e363 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 11 Dec 2014 18:10:06 +0100 Subject: [PATCH 0088/1172] removed build stats --- .../MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb | 28 ------------------- 1 file changed, 28 deletions(-) diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb index 9912401ae1..14ede40f79 100644 --- a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 1.15.2 on 2014-12-11_18-03-37 # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) @@ -40,30 +39,3 @@ sanity_check_paths = { } moduleclass = 'bio' - - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "1.15.2", - "easybuild-easyblocks_version": "1.15.2", - "timestamp": 1418317417, - "build_time": 55.91, - "install_size": 412887, - "command_line": ['--buildpath=/tmp/easybuild', '--installpath=/import/bc2', '--modules-tool=Lmod', '--repositorypath=/import/bc2/soft/centos6/installation_recipes/installed_easyconfigs_sandybridge', '--sourcepath=/import/bc2/soft/source', '--subdir-software=apps', 'MACS-1.4.2-1-goolf-1.4.10.eb'], - "modules_tool": ('Lmod', '/import/bc2/soft/system/apps/lmod/lmod/libexec/lmod', '5.7.4'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2601.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/import/bc2/apps/GCC/4.7.2/libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran,lto --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=/import/bc2/apps/GCC/4.7.2 --with-local-prefix=/import/bc2/apps/GCC/4.7.2; Thread model: posix; gcc version 4.7.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "login11", - "kernel_name": "Linux", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.5", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 22 2013, 12:16:22) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/import/bc2/apps/GCC/4.7.2/bin/gcc", - "system_python_path": "/import/bc2/apps/Python/2.7.5-goolf-1.4.10/bin/python", -}] -- GitLab From f1e903f9e87acbcc338bff1f99dc0c79a15a66b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 16 Dec 2014 09:20:04 +0100 Subject: [PATCH 0089/1172] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b5c98f2a72..f0f5501b84 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'PostgreSQL' version = '9.3.5' -- GitLab From fbe18fa83394133ca1a1601ec15a01396a4a7280 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:04 +0100 Subject: [PATCH 0090/1172] All deps for gnuplot 5 with intel-2015a --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 29 +++++++++++++++++ .../e/expat/expat-2.1.0-intel-2015a.eb | 15 +++++++++ .../fontconfig-2.11.1-intel-2015a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.5.5-intel-2015a.eb | 21 +++++++++++++ .../libjpeg-turbo-1.4.0-intel-2015a.eb | 24 ++++++++++++++ .../l/libpng/libpng-1.6.16-intel-2015a.eb | 19 ++++++++++++ .../n/NASM/NASM-2.11.06-intel-2015a.eb | 31 +++++++++++++++++++ .../p/pixman/pixman-0.32.6-intel-2015a.eb | 20 ++++++++++++ 8 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb new file mode 100644 index 0000000000..e43e75307f --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('freetype', '2.5.5'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +# 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/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb new file mode 100644 index 0000000000..0eb1188648 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb new file mode 100644 index 0000000000..a8f2612b6a --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb new file mode 100644 index 0000000000..3f93bd6070 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -0,0 +1,21 @@ +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': 'intel', 'version': '2015a'} + +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/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb new file mode 100644 index 0000000000..639a4e904b --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb new file mode 100644 index 0000000000..23292508e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb new file mode 100644 index 0000000000..88003caecd --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.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 = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb new file mode 100644 index 0000000000..480001289a --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 2bdc74f8dacb175fddf22ea06495f54ece3236fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:28 +0100 Subject: [PATCH 0091/1172] Gnuplot 5 for intel-2014b and intel-2015a --- .../g/gnuplot/gnuplot-5.0.0-intel-2014b.eb | 35 +++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.0-intel-2015a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb new file mode 100644 index 0000000000..e30d4a22d3 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb new file mode 100644 index 0000000000..8f7d80279e --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 441dd17e18b9dffa536fe73cd3aa5ee70db3642e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:18:56 +0100 Subject: [PATCH 0092/1172] Added autoconf for intel 2015a --- .../a/Autoconf/Autoconf-2.69-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb new file mode 100644 index 0000000000..a3c280daab --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb @@ -0,0 +1,25 @@ +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': '2015a'} + +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' -- GitLab From d24528dc73eec74272050e5dcf06876c35a902a5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:19:13 +0100 Subject: [PATCH 0093/1172] Updated cairo to work around pthread detection issues --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 6 ++++++ .../c/cairo/cairo-1.12.18-pthread-check.patch | 17 +++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index e43e75307f..d051b99544 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,6 +23,12 @@ dependencies = [ ('bzip2', '1.0.6'), ] +builddependencies = [('autoconf', '2.69')] + +patches = ['cairo-1.12.18-pthread-check.patch'] + +preconfigopts = " autoconf configure.ac > configure && " + # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC configopts = "--enable-symbol-lookup=no" diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch new file mode 100644 index 0000000000..20821e7211 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -0,0 +1,17 @@ +# Make sure the configure script doesn't fail over a 'no version information available' warning +# by wpoely86@gmail.com +diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.cairo.m4 +--- cairo-1.12.18.orig/build/aclocal.cairo.m4 2013-03-15 21:29:27.000000000 +0100 ++++ cairo-1.12.18/build/aclocal.cairo.m4 2015-01-14 14:08:01.000000000 +0100 +@@ -101,9 +101,9 @@ + $1 + AC_LINK_IFELSE( + [AC_LANG_SOURCE([$_compile_program])], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=yes], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=no]) + + if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 9701985a5c4b5e603263bed5d39ff6bfa557dc5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:20:55 +0100 Subject: [PATCH 0094/1172] Fix typo in cairo --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index d051b99544..c3b27fffcb 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('autoconf', '2.69')] +builddependencies = [('Autoconf', '2.69')] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 22feb6bfe7fafec7f5e1dbf667ea9aff4ef0e70e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 16:52:23 +0100 Subject: [PATCH 0095/1172] Stupid stupid stupid error in patch --- .../easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch index 20821e7211..9019afb946 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -8,10 +8,10 @@ diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.c AC_LINK_IFELSE( [AC_LANG_SOURCE([$_compile_program])], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=yes], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=no]) if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 8024913b322f6757649f0c2e12594a3a3188973b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Jan 2015 17:13:38 +0100 Subject: [PATCH 0096/1172] Enable UTF-8 in ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 3bcfd50e3f..52d037a115 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,4 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# enable UTF-8 version of ncurses +configopts = '--enable-widec ' + moduleclass = 'devel' -- GitLab From 6aae2b595d2f9e7d909a5f6cf08ff98f6e3492f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Jan 2015 17:52:00 +0100 Subject: [PATCH 0097/1172] Build libncurses and libncursesw --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 52d037a115..0cd975654f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# enable UTF-8 version of ncurses -configopts = '--enable-widec ' +# build the normal library and the UTF-8 version +configopts = ['', '--enable-widec '] moduleclass = 'devel' -- GitLab From 04539511825fd537874a74a8d2bc8157891c4f0e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 24 Jan 2015 13:53:57 +0100 Subject: [PATCH 0098/1172] Another try for ncursesw --- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 0cd975654f..b52538d409 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,7 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# build the normal library and the UTF-8 version -configopts = ['', '--enable-widec '] +configopts = [ +# the regular version + '--enable-pc-files', +# the UTF-8 enabled version (ncursesw) + '--enable-pc-files --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] moduleclass = 'devel' -- GitLab From 8752a28c823ec55f6a21f615e49a45877230642a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 24 Jan 2015 14:10:27 +0100 Subject: [PATCH 0099/1172] drop pkg-config in ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index b52538d409..3ec3f49a07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,9 +14,9 @@ sources = [SOURCE_TAR_GZ] configopts = [ # the regular version - '--enable-pc-files', + '', # the UTF-8 enabled version (ncursesw) - '--enable-pc-files --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' -- GitLab From 35266d8655bfa26924a951417b616c6f08716a21 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Jan 2015 20:24:01 +0100 Subject: [PATCH 0100/1172] Fix remarks --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 3ec3f49a07..867d190ac8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -13,9 +13,9 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] configopts = [ -# the regular version + # default build, no custom configure options '', -# the UTF-8 enabled version (ncursesw) + # the UTF-8 enabled version (ncursesw) '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -- GitLab From 5d2d1b0b9cc82f64abf00ff3b5d87caaaf46ef86 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Jan 2015 20:31:40 +0100 Subject: [PATCH 0101/1172] Enable for ncursesw in all ncurses easyconfigs --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 7 +++++++ 40 files changed, 280 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 3522f8a87b..612e7244e4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index f954a9b12a..0bc9dc079e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 6a10d2ec63..30ff4e9d12 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 4913ef008f..d637ceb09f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -14,6 +14,13 @@ sources = [SOURCE_TGZ] # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 8b7d3a2416..ecedc6d59c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1632ef23de..44555aa4d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 43375f2a29..6b107ae408 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index ad58285a85..eeca718a41 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index f972b6a4ff..7ed33f8631 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5f56a55621..b72a2c5545 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index cd59ae4ab3..ee2b0ee573 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 52e0aac9ea..e7e371cbeb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 78b7618284..fc7e428415 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index b4ea71f97f..caaf4d94b5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 2f9501c9ae..cd83ef60ce 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index 15745294d9..fc5b9a327c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 062cbaeab6..ef9c9fdf56 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a372492a64..1e42213c88 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -12,6 +12,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 38b356d5e1..1a4bf4b720 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 947e8e3afa..33d8114b0a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 4084c938c1..38625bc5af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 33bb21037f..9cd547f787 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index e67f480463..f6221718e5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 5a698183f4..794f3cf9ff 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 4e33e95089..51c7c4637d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index c0284ad94f..0da2bc399e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 95388cfc5b..51e89fabbe 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 731485e77b..efe819bc41 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 8cb79c351b..b1d6ed583b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index ee127c7a3c..7acb72a025 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 020778b318..411d761488 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index a81155369d..e647ee8ca9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 84c486d4d9..b4ba551660 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ab5e8538f3..2a4e97a56d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -14,4 +14,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 2a7094da21..5585b5f946 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 4aface2738..3084b14d4f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8..51bee3bd1f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -19,4 +19,11 @@ configopts = [ '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 9963e053c2..3442fd88ba 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index decfe9bc04..e40599e242 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index f4b42632c9..75c66a9c2a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' -- GitLab From d2cd0fe9eb7b32c8354c03f184e05fed63348885 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:45:08 +0100 Subject: [PATCH 0102/1172] We are gonna drop the block for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 2 ++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 2 ++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 2 ++ 40 files changed, 80 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 612e7244e4..c1bbc1841f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 0bc9dc079e..4e4d33f99e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 30ff4e9d12..175c730746 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index d637ceb09f..5d25cf6a2c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index ecedc6d59c..74e5f9d664 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 44555aa4d2..54ecc2aa20 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 6b107ae408..923b64a2b1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index eeca718a41..d656ee0065 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 7ed33f8631..2a34cb02bd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index b72a2c5545..7172901875 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index ee2b0ee573..8dcd07e56e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index e7e371cbeb..fe078dec07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index fc7e428415..f56f2e2f3f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index caaf4d94b5..fbcfb30bca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index cd83ef60ce..8a0a0a6686 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index fc5b9a327c..ef641196aa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index ef9c9fdf56..bead5d5548 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 1e42213c88..a80072cffd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 1a4bf4b720..16c3de6193 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 33d8114b0a..fe409e6bef 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 38625bc5af..109ffe0762 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 9cd547f787..013e826233 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index f6221718e5..d98d2224a8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 794f3cf9ff..04d9e09dc8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 51c7c4637d..cbbffabdf6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 0da2bc399e..d2814a64a5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 51e89fabbe..312ebedf9f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index efe819bc41..2fe6cb142e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index b1d6ed583b..e3bb6acc60 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 7acb72a025..22f9c52166 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 411d761488..738094a8e2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index e647ee8ca9..cda26334d3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index b4ba551660..b2f405273f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 2a4e97a56d..c42c316754 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 5585b5f946..d205c60702 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 3084b14d4f..7893f29d3f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8..94883afa9c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 3442fd88ba..b9054c4126 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index e40599e242..980ddeeb1b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 75c66a9c2a..a0cd6ba12f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' -- GitLab From c192f7c59f8286b812de97bdbf7ed49fff7fafcf Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:49:50 +0100 Subject: [PATCH 0103/1172] Add darwin patch everywhere for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 5 ++++- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 3 +++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 3 +++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 3 +++ 40 files changed, 121 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index c1bbc1841f..d6014c322a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 4e4d33f99e..340e451aec 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 175c730746..04ba4525a8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 5d25cf6a2c..1ebda09767 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -11,10 +11,13 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} toolchainopts = {'optarch': True, 'pic': True} -sources = [SOURCE_TGZ] # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +sources = [SOURCE_TGZ] + +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ # default build, no custom configure options diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 74e5f9d664..d0b0145611 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 54ecc2aa20..463bfe470b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 923b64a2b1..f717055d33 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index d656ee0065..10513a3220 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 2a34cb02bd..c713d9a1f0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 7172901875..de5fe067af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 7a01c335e9..1120c00075 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -17,6 +17,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index fe078dec07..6fe83c6278 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index f56f2e2f3f..3b2a8be253 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index fbcfb30bca..016a0e7ba7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 8a0a0a6686..ad1db40db0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index ef641196aa..b7eac5dc3b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index bead5d5548..32697687bd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a80072cffd..8f42fa1df4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 16c3de6193..6adba21388 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index fe409e6bef..71be12db82 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 109ffe0762..b2bd02a79f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 013e826233..f43ac7b793 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index d98d2224a8..d485cb49cb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 04d9e09dc8..fac41c78c8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index cbbffabdf6..3b5e2ad161 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index d2814a64a5..9591d9dd15 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 312ebedf9f..807f4ac478 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 2fe6cb142e..0b83eb7d69 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index e3bb6acc60..35aab70c78 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 22f9c52166..440b759444 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 738094a8e2..de9ab95d93 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index cda26334d3..dd539c41ee 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index b2f405273f..96658e9de5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index c42c316754..fbd2501cb3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index d205c60702..77555deb61 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 7893f29d3f..5e21a72951 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 94883afa9c..4d5679832e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index b9054c4126..edb162762e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 980ddeeb1b..f9e31b4951 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index a0cd6ba12f..531773e338 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', -- GitLab From a70b0dbf432dc6396924c5fdbf5a92e236c6961f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:54:00 +0100 Subject: [PATCH 0104/1172] Use same configopts as in easyblock --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 6 +++--- 40 files changed, 120 insertions(+), 120 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index d6014c322a..bb5656e2a6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 340e451aec..c886fe843f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 04ba4525a8..ebbfaa4116 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 1ebda09767..5c607404c1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index d0b0145611..1a855ba2bc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 463bfe470b..5323795d31 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index f717055d33..98be0d4c70 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 10513a3220..d4b7a59d96 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index c713d9a1f0..998a5e97ab 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index de5fe067af..53f116fa2e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 1120c00075..a086acf239 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -21,10 +21,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 6fe83c6278..7e4ecbfbb4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 3b2a8be253..55ed8d26f6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 016a0e7ba7..5ee673d106 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index ad1db40db0..e805cd9d17 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index b7eac5dc3b..d6f07984c3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 32697687bd..80481a982f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 8f42fa1df4..ef647ff36e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 6adba21388..b25da04d34 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 71be12db82..465f64143f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index b2bd02a79f..e60406ef3b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index f43ac7b793..2342cdf598 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index d485cb49cb..8131a3deb8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index fac41c78c8..4320090d62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 3b5e2ad161..058e2d911f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 9591d9dd15..3fc4dbeb15 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 807f4ac478..bcd27e8b03 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 0b83eb7d69..e757256ace 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 35aab70c78..40ba8d73af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 440b759444..1483b7bf55 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index de9ab95d93..fb0453b4df 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index dd539c41ee..583d73732b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 96658e9de5..1eb6d03b2a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index fbd2501cb3..ada5615af2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 77555deb61..b24af21a1d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 5e21a72951..282c1bb362 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 4d5679832e..9423467931 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index edb162762e..40ddbfa412 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index f9e31b4951..868c6a2548 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 531773e338..76893f1192 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' -- GitLab From 765d0211bafdbff648e3571c80867a89e292dd82 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:57:57 +0100 Subject: [PATCH 0105/1172] Move patch comment into patch --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 1 - .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 1 - .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 2 -- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch | 2 ++ 41 files changed, 2 insertions(+), 41 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index bb5656e2a6..54e14d2a5b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index c886fe843f..c1f0ff7fd5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index ebbfaa4116..875f56a51e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 5c607404c1..ce47ae5e0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 1a855ba2bc..98c94f5e9e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 5323795d31..1bf10071f6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 98be0d4c70..2b21c09a91 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index d4b7a59d96..192d513a80 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 998a5e97ab..974b0ae6ed 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 53f116fa2e..2d67efa2d5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index a086acf239..1d7c5cc5a2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -8,7 +8,6 @@ description = """The Ncurses (new curses) library is a free software emulation o 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.""" -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] toolchain = {'name': 'GCC', 'version': '4.8.2'} @@ -17,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 7e4ecbfbb4..4b3eee0442 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 55ed8d26f6..8181599cdf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 5ee673d106..4db2c80086 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index e805cd9d17..d17f763573 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index d6f07984c3..f3056c6cc3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 80481a982f..6482090fe7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index ef647ff36e..729623bbc5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index b25da04d34..783353a5e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 465f64143f..1f7cb3f66e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index e60406ef3b..432e92f67a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 2342cdf598..23ac474bfd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index 8131a3deb8..7b855b2439 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 4320090d62..0aaaa39fd8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 058e2d911f..988166fe3c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 3fc4dbeb15..101d3a39be 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index bcd27e8b03..509cfc629d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index e757256ace..e4a369e4a4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 40ba8d73af..9a1bd44ae0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 1483b7bf55..dbc54a911d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index fb0453b4df..97ad47cdc7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 583d73732b..350c62963e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 1eb6d03b2a..ad40bd7b81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ada5615af2..3421c52995 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index b24af21a1d..27921a13b6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 282c1bb362..3059b1ba1a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 9423467931..ff0d85d604 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 40ddbfa412..1e51ebbe9c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 868c6a2548..bc591b2935 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 76893f1192..d48f6b822e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index cbc78d120b..19a1f77d5b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,3 +1,5 @@ +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +# by Fotis --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ -- GitLab From f6d433f619a6eeba900ef89d1683db553b258794 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 10:03:14 +0100 Subject: [PATCH 0106/1172] New sanity check for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index ff0d85d604..4912fd41da 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -23,4 +23,14 @@ configopts = [ '--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' -- GitLab From 070cce48b60e412dff94e34b1b9ac74dfc9429ef Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 10:18:38 +0100 Subject: [PATCH 0107/1172] Added sanity check everywhere --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 10 ++++++++++ .../ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 10 ++++++++++ 39 files changed, 390 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 54e14d2a5b..6d40fe65a5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index c1f0ff7fd5..7d2df71a8f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 875f56a51e..a971bf0cc9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index ce47ae5e0b..360335ba07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 98c94f5e9e..021bbd904f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1bf10071f6..439c4ca406 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 2b21c09a91..1fcb38e69b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 192d513a80..399dc72d43 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 974b0ae6ed..bcf8a1dcfa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 2d67efa2d5..d967731cf4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 1d7c5cc5a2..9608f82f81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -25,4 +25,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 4b3eee0442..6bf4c2b332 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 8181599cdf..6313c884fc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 4db2c80086..727175a0e9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index d17f763573..26e6ab54bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index f3056c6cc3..c993267096 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 6482090fe7..38361f94f7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 729623bbc5..b057182b0c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -26,4 +26,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +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/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 783353a5e6..d67bdf2770 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 1f7cb3f66e..169534ccd8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 432e92f67a..7e1f5ce19f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 23ac474bfd..2df180dac8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index 7b855b2439..c31fdc08ca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 0aaaa39fd8..bfba6b87fe 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 988166fe3c..76b20bd13a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 101d3a39be..1cb1b2fa6b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 509cfc629d..cf54b65a18 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index e4a369e4a4..7ee6110e8d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 9a1bd44ae0..5753a19c6f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index dbc54a911d..7466ea8529 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 97ad47cdc7..2df3b61306 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 350c62963e..0d8611a193 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index ad40bd7b81..ce62d53ca0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 3421c52995..017c395992 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -25,4 +25,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 27921a13b6..b6a67863ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 3059b1ba1a..edb943229c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 1e51ebbe9c..389a334b0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index bc591b2935..ab5729d6df 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -23,4 +23,14 @@ configopts = [ '--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/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index d48f6b822e..1a23dd3813 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -23,4 +23,14 @@ configopts = [ '--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' -- GitLab From f4c8416d21a83206b93adef5d30cc93331af8243 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:38:11 +0000 Subject: [PATCH 0108/1172] Building an older version of Cufflinks for users that like the older format --- .../Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 42 +++++++++++++++++ .../c/Cufflinks/cufflinks-1.3.0-ldflags.patch | 45 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch 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 new file mode 100644 index 0000000000..2eca2eb6ac --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +## +# 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 +## + +name = 'Cufflinks' +version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch new file mode 100644 index 0000000000..9c2bd9e9a2 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch @@ -0,0 +1,45 @@ +diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure +--- cufflinks-1.3.0/configure 2012-01-02 13:36:44.000000000 +0000 ++++ cufflinks-1.3.0_patched/configure 2015-01-27 18:32:24.810282390 +0000 +@@ -6386,7 +6386,8 @@ + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++user_LDFLAGS="$LDFLAGS" ++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + + # Checks for structures/functions that can be used to determine system memory + echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5 +diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in +--- cufflinks-1.3.0/src/Makefile.in 2012-01-02 13:36:43.000000000 +0000 ++++ cufflinks-1.3.0_patched/src/Makefile.in 2015-01-27 18:20:02.944386541 +0000 +@@ -438,24 +438,24 @@ + # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@ + cufflinks_SOURCES = cufflinks.cpp + cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) ++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) + cuffcompare_SOURCES = cuffcompare.cpp + cuffcompare_LDADD = libgc.a + gffread_SOURCES = gffread.cpp + gffread_LDADD = libgc.a + cuffdiff_SOURCES = cuffdiff.cpp + cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + gtf_to_sam_SOURCES = gtf_to_sam.cpp + gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + #cuffcluster_SOURCES = cuffcluster.cpp + #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) + #cuffcluster_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + compress_gtf_SOURCES = compress_gtf.cpp + compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + all: all-am + + .SUFFIXES: -- GitLab From 6f4ac9178ba8ad044f765c67cdc1b215b03cb18f Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:46:15 +0000 Subject: [PATCH 0109/1172] removing a bad comment --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 2eca2eb6ac..60d2ee4a72 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 @@ -11,7 +11,7 @@ ## name = 'Cufflinks' -version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') +version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -- GitLab From 55c4a267adec324bb0ba120fcc5c08921e0481a6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:18:33 +0000 Subject: [PATCH 0110/1172] some style changes --- .../c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 7 +++++-- ...nks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} | 0 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Cufflinks/{cufflinks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} (100%) 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 60d2ee4a72..d03c8b241d 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 @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -29,7 +29,10 @@ dependencies = [ ('zlib', '1.2.7'), ] -patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] +patches = [ + 'Cufflinks_GCC-4.7.patch', + 'cufflinks-1.x-ldflags.patch' +] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch similarity index 100% rename from easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch rename to easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch -- GitLab From 6bf1b6cd4d227abefce167ec9eaf533d5ad0098c Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:21:24 +0000 Subject: [PATCH 0111/1172] whoops, inverted wrong line --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index d03c8b241d..96199f4bf2 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchainopts = {'optarch': True, 'pic': True} toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -34,8 +34,8 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From 19e1b5d2c5e2d4b897291483f9469a641a06e170 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 28 Jan 2015 09:10:38 +0100 Subject: [PATCH 0112/1172] Added intel easyconfig for SAMtools --- .../s/SAMtools/SAMtools-1.1-intel-2015a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb new file mode 100644 index 0000000000..91e58c27f0 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.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 +# 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 +## + +name = 'SAMtools' +version = '1.1' + +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' -- GitLab From 45bf598d8b7ac24c166c738bad6a8a8a3094be6c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 17:26:33 +0100 Subject: [PATCH 0113/1172] Added some additional comment in the MacOSX patch --- .../easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index 19a1f77d5b..293f47532a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,5 +1,5 @@ # in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html -# by Fotis +# tried/proposed by Fotis, meant for MacOSX compatible ncurses builds... --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ -- GitLab From 997f1baf47f0ce8120d6d442d130ca08269b752d Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:34:46 +0000 Subject: [PATCH 0114/1172] a foss-2015a version of Cufflinks-2.2.1 --- .../Boost-1.55.0-foss-2015a-Python-2.7.9.eb | 25 ++++++++++++++++ .../c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 29 +++++++++++++++++++ .../e/Eigen/Eigen-3.2.3-foss-2015a.eb | 14 +++++++++ .../s/SAMtools/SAMtools-0.1.19-foss-2015a.eb | 21 ++++++++++++++ 4 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..88a81a73e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +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} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..7ae5cdce38 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.9'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000..a2767dc205 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.3' + +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': '2015a'} +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/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb new file mode 100644 index 0000000000..c7a055062e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 9d7b3d81fb4b342881becb00d0f9f779523b0864 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:38:28 +0000 Subject: [PATCH 0115/1172] switching order of config and preconfig --- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 7ae5cdce38..d0372e6f70 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 @@ -18,8 +18,8 @@ dependencies = [ ('zlib', '1.2.8'), ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From c6a3e90a717bc1766ccf7b314c7fc5e72a8683d0 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:38:40 +0100 Subject: [PATCH 0116/1172] Added foss easyconfig for libffi --- .../l/libffi/libffi-3.2.1-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb new file mode 100644 index 0000000000..17a9f263e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.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': '2015a'} + +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' -- GitLab From 7ebc21cd01ea2cafb635489e1c3596490725f174 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:47:27 +0100 Subject: [PATCH 0117/1172] Added foss easyconfig for gettext --- .../g/gettext/gettext-0.19.4-foss-2015a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb new file mode 100644 index 0000000000..51c244d3ef --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 681107aa60b510d71b2640f4fc1aaf4760d933a9 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:49:54 +0100 Subject: [PATCH 0118/1172] Added foss easyconfig for GLib --- .../g/GLib/GLib-2.42.1-foss-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb new file mode 100644 index 0000000000..167d8fc75b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.42.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From e1e346e87c0c6ee6c94186aa7ee80a9ebbc6c2d3 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:12:39 +0100 Subject: [PATCH 0119/1172] Added foss easyconfig for Qt --- .../easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb new file mode 100644 index 0000000000..c226c3cb72 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.42.1')] + +moduleclass = 'devel' -- GitLab From c4cff509183f97b26b3c49e5f45c6f7c83b1694e Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:18:29 +0100 Subject: [PATCH 0120/1172] Added foss easyconfig for Cube --- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb new file mode 100644 index 0000000000..eac6956fc7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -0,0 +1,39 @@ +# 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 = 'EB_Score_minus_P' + +name = "Cube" +version = "4.3" + +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': '2015a'} + +# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] + + +# patches = ['Cube-4.2_fix-Qt-version-check.patch'] + +dependencies = [('Qt', '4.8.6')] + +configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From cff53b3ba27ce7f492b01a8dd00856c3c873e436 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:22:20 +0100 Subject: [PATCH 0121/1172] Added foss easyconfig for OTF2 --- .../o/OTF2/OTF2-1.5.1-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb new file mode 100644 index 0000000000..d09eb89527 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.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/ +## +easyblock = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.5.1" + +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 will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 21d27710908a65227ffb63e4026ad8d3a5163557 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:31:29 +0100 Subject: [PATCH 0122/1172] Added foss easyconfig for OPARI2 --- .../o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb new file mode 100644 index 0000000000..ad5274512f --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.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/ +## +easyblock = 'ConfigureMake' + +name = "OPARI2" +version = "1.1.2" + +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': '2015a'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From dab4edf5dc4a2088ef5c942a722afdb164927946 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:42:49 +0100 Subject: [PATCH 0123/1172] Added foss easyconfig for PAPI --- .../p/PAPI/PAPI-5.4.0-foss-2015a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb new file mode 100644 index 0000000000..c9ba2ffbaf --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-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 = '5.4.0' + +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 03995320a28a9c681637feec5b7a274c25bad042 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:53:37 +0100 Subject: [PATCH 0124/1172] Added foss easyconfig for PDT --- .../easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb new file mode 100644 index 0000000000..81d6197602 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -0,0 +1,50 @@ +# 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 = "PDT" +version = "3.20" + +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': '2015a'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' -- GitLab From 43ed8d5e7e43a2c116e96329a7b7b5087e6f04df Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 16:07:56 +0100 Subject: [PATCH 0125/1172] Added foss easyconfig for Score-P --- .../s/Score-P/Score-P-1.4-foss-2015a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb new file mode 100644 index 0000000000..68a27ad6ea --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -0,0 +1,45 @@ +# 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/ +## +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '1.4' + +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': '2015a'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.25', '', ('GCC', '4.9.2')), + ('Cube', '4.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.5.1'), + ('PAPI', '5.4.0'), + ('PDT', '3.20'), +] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 2589d6e9ddc9371fc2ed0ae7301f2638451259e8 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 16:14:29 +0100 Subject: [PATCH 0126/1172] Added foss easyconfig for Scalasca --- .../s/Scalasca/Scalasca-2.2-foss-2015a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb new file mode 100644 index 0000000000..c088e07420 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb @@ -0,0 +1,36 @@ +# 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 = 'EB_Score_minus_P' + +name = "Scalasca" +version = "2.2" + +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': '2015a'} +toolchainopts = {"usempi": True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version)s/dist'] + +dependencies = [ + ('Cube', '4.3'), + ('OTF2', '1.5.1'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 5a9644723c9e2093444c854d563d818bf1004582 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 17:04:09 +0100 Subject: [PATCH 0127/1172] Removed comment as per request --- easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index eac6956fc7..55bce806bc 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -20,7 +20,6 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'foss', 'version': '2015a'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] -- GitLab From 3ab998c8b6946b302d44704c52a013dd7eab7ab8 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 17:05:32 +0100 Subject: [PATCH 0128/1172] Fixed style issues as per request --- easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index 81d6197602..e261f444df 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -31,6 +31,8 @@ prefix_opt = '-prefix=' # -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc configopts = '-GNU' +skipsteps = ['build'] + keeppreviousinstall = True # notes by Bernd Mohr @@ -40,8 +42,6 @@ sanity_check_paths = { 'dirs': [], } -skipsteps = ['build'] - modextrapaths = { 'PATH': "x86_64/bin", 'LD_LIBRARY_PATH': "x86_64/lib", -- GitLab From a9cfa39894c7c672c3dc34abdc96281ecac2154c Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 6 Feb 2015 14:42:08 +0100 Subject: [PATCH 0129/1172] scanms easyconfig --- .../SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..76fe9f0898 --- /dev/null +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,44 @@ +# 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 = 'PerlModule' + +name = 'SCANMS' +version = '2.02' + +homepage = 'http://compbio.ucmerced.edu/ardell/software/scanms/' +description = """SCANMS is an open source utility written in Perl that works in + conjunction with Richard Hudson’s coalescent simulator MS to do parametric + bootstrapping of a sliding window analysis of neutrality test statistics. + Currently supported statistics are Tajima’s D and Fu and Li’s D* and F*. + Its output of a joint distribution of window minima and maxima may then be + used to correct for multiple comparisons in such analyses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compbio.ucmerced.edu/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# workaround so sanity check in the PerlModule easyblock works. +# Just check the existence of a perl core module +options = {'modulename': 'POSIX'} + +sanity_check_paths = { + 'files': ["bin/scanms"], + 'dirs': [""] +} + +# copy all the documentation provided in the tarball to install directory +postinstallcmds = ["cp -r %(builddir)s/*/{README,SCANMS.pdf,scanms.doc.html} %(installdir)s"] + +moduleclass = 'bio' -- GitLab From 9ea1a7dedcdd0d2313fc7b50c5e61755605159cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Feb 2015 22:53:06 +0100 Subject: [PATCH 0130/1172] add easyconfig for bundle of extra R extensions (PoC) --- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb new file mode 100644 index 0000000000..e71e3abf1d --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'R-extra' +rver = '3.1.2' +version = '%s-1.0.0' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('GMP', '6.0.0a'), # for gmp +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('gmp', '0.5-12', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' -- GitLab From 32d6b80d049418487f1f5fa325f80c746f2f0ed7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Feb 2015 09:31:12 +0100 Subject: [PATCH 0131/1172] add easyconfig for JUBE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb new file mode 100644 index 0000000000..0044a1ec87 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -0,0 +1,22 @@ +easyblock = "VersionIndependentPythonPackage" + +name = "JUBE" +version = "2.0.3" + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +sources = [SOURCELOWER_TAR_GZ] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 93106b542c5677e5dce0f390969501c2f1d978a3 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 16 Feb 2015 15:28:32 +0100 Subject: [PATCH 0132/1172] Update download URLs for Qt --- easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb index c226c3cb72..2111ce217a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -7,8 +7,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/', + 'http://master.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From 787816f2e5c7615aecdbae480f33d70a6254f02f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:18:56 +0100 Subject: [PATCH 0133/1172] Adjusted URL, added checksum, and tweaked build --- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index 55bce806bc..c0a4d9c729 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -21,18 +21,22 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] - -# patches = ['Cube-4.2_fix-Qt-version-check.patch'] +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] dependencies = [('Qt', '4.8.6')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" - sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } +# If all prerequisites for the Cube Java reader are available on the system, +# parallel builds will fail. Alternatively, disable the Java reader using +# configopts = "--without-java-reader" +maxparallel = 1 + moduleclass = 'perf' -- GitLab From 8af6b22c2d786586ec127d6c3cde869a73e2a52f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:20:08 +0100 Subject: [PATCH 0134/1172] Added checksum --- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 5 ++++- easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index ad5274512f..6a2ab2df29 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -19,10 +19,13 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'foss', 'version': '2015a'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +checksums = [ + '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz +] + sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], 'dirs': [], diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index d09eb89527..4f583c01b1 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -18,10 +18,13 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'foss', 'version': '2015a'} -# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +checksums = [ + '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz +] + sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], -- GitLab From 7807884a30458c3c50b966ddb1ab913a706b27db Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:20:42 +0100 Subject: [PATCH 0135/1172] Removed outdated comment --- easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index e261f444df..124698a037 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -20,7 +20,6 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'foss', 'version': '2015a'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -- GitLab From 4e2f20cbf247302abf58968180c92f67daab017f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:21:13 +0100 Subject: [PATCH 0136/1172] Remved outdated comment, add checksum, and tweaked build --- easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index 68a27ad6ea..91b0941367 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -20,10 +20,13 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +checksums = [ + '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz +] + # compiler toolchain depencies dependencies = [ ('binutils', '2.25', '', ('GCC', '4.9.2')), @@ -34,8 +37,6 @@ dependencies = [ ('PDT', '3.20'), ] -maxparallel = 1 - sanity_check_paths = { 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], -- GitLab From c5ac4f05ae2026c706758d3abd32004784c80e14 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:25:22 +0100 Subject: [PATCH 0137/1172] Adjusted URL and added checksum --- easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb index c088e07420..55d127b2f7 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb @@ -21,7 +21,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version)s/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + '06e0380c612811a1ff9c183fed9331a9', # scalasca-2.2.tar.gz +] dependencies = [ ('Cube', '4.3'), -- GitLab From c80efece700ec06ab718e2f7c84402dd66b3298b Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 19 Feb 2015 12:47:49 +0100 Subject: [PATCH 0138/1172] added PeakSeq-1.3-goolf-1.4.10.eb --- .../p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..0a7acf4ed3 --- /dev/null +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.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 = "PeakSeq" +version = "1.3" + +homepage = 'http://info.gersteinlab.org/PeakSeq' +description = """ PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq + experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from + a control experiment and outputs a file with peak regions ranked with increasing Q-values.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/'] +sources = ['%(name)s.zip'] + +# as the tarball doesn't contain the version we verify the checksum to be sure +# we don't download a newer version and consider it as 1.3 +checksums = [('md5', '32b4d71b2ec9455c7db69516b1bd4910')] + +buildopts = ' CC="$CXX"' + +files_to_copy = ["bin", "README" ] + +sanity_check_paths = { + 'files': ["bin/PeakSeq"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 7f0f28e1bf0c6a5bd1ea745a670202fe09246408 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 27 Feb 2015 14:39:05 +0100 Subject: [PATCH 0139/1172] dummy --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From c1b4a70e085d719044bc78354630bb696d2d81a3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 27 Feb 2015 16:05:47 +0100 Subject: [PATCH 0140/1172] netCDF and deps foss-2014b --- .../b/Bison/Bison-3.0.2-foss-2014b.eb | 22 +++++++++++++ .../c/CMake/CMake-3.0.0-foss-2014b.eb | 22 +++++++++++++ .../c/cURL/cURL-7.37.1-foss-2014b.eb | 27 ++++++++++++++++ .../d/Doxygen/Doxygen-1.8.7-foss-2014b.eb | 18 +++++++++++ .../f/flex/flex-2.5.39-foss-2014b.eb | 14 ++++++++ .../h/HDF5/HDF5-1.8.13-foss-2014b.eb | 21 ++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 23 +++++++++++++ .../netCDF-C++4-4.2.1-foss-2014b.eb | 24 ++++++++++++++ .../netCDF-Fortran-4.4.0-foss-2014b.eb | 18 +++++++++++ .../n/netCDF/netCDF-4.3.2-foss-2014b.eb | 32 +++++++++++++++++++ .../easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb | 23 +++++++++++++ 11 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb new file mode 100644 index 0000000000..821e3cc963 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'foss', 'version': '2014b'} + +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-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000..872f8b4d7d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': 'foss', 'version': '2014b'} + +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' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb new file mode 100644 index 0000000000..00fec4f4d1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb new file mode 100644 index 0000000000..9604d1fe3e --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': 'foss', 'version': '2014b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb new file mode 100644 index 0000000000..6a24b017aa --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.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': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb new file mode 100644 index 0000000000..2af8e449bf --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2014b'} +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 = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' 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 new file mode 100644 index 0000000000..94ec58056b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.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': 'foss', 'version': '2014b'} + +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/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb new file mode 100644 index 0000000000..5fcb22ae6f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.2.1' + +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': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] + +dependencies = [('netCDF', '4.3.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb new file mode 100644 index 0000000000..4d00f104ad --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +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': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index e69de29bb2..94c5d118ea 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -0,0 +1,32 @@ +name = 'netCDF' +version = '4.3.2' + +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': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' + diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb new file mode 100644 index 0000000000..9d1f75c5eb --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.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': 'foss', 'version': '2014b'} +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.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 77867574f8ac0fd886564d1d20084236399f519f Mon Sep 17 00:00:00 2001 From: "Balazs Hajgato (hajgato@ulb.ac.be)" Date: Mon, 2 Mar 2015 07:09:33 +0100 Subject: [PATCH 0141/1172] Use external HDF5 h5(p)cc --- .../n/netCDF/netCDF-4.3.2-foss-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-intel-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-intel-2015a.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-parallel-HDF.patch | 21 +++++++++++++++++++ 4 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index 94c5d118ea..ffb64828a3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 5ab91b52fe..172783a9aa 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index bb04604455..0456d513c3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch new file mode 100644 index 0000000000..d097592f15 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch @@ -0,0 +1,21 @@ +#If a system installed sequential HDF5 exist and we use an external +#parallel HDF5 intsllation then the system installed h5cc will be used +#instead of the external h5pcc. Inspiration from netCDF 4.3.3.1 +#B. Hajgato March 1st 2015 +--- netcdf-4.3.2/CMakeLists.txt.org 2014-04-23 23:35:20.000000000 +0200 ++++ netcdf-4.3.2/CMakeLists.txt 2015-03-01 21:07:55.000000000 +0100 +@@ -637,8 +637,13 @@ + ENDIF(NOT MSVC) + + # Assert HDF5 version. ++ IF(HDF5_IS_PARALLEL) ++ SET(HDF5_CC h5pcc) ++ ELSE() ++ SET(HDF5_CC h5cc) ++ ENDIF() + SET(HDF5_VERSION_REQUIRED 1.8.6) +- execute_process(COMMAND sh -c "h5cc -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" ++ execute_process(COMMAND sh -c "${HDF5_CC} -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" + OUTPUT_VARIABLE HDF5_VERSION + ERROR_QUIET + ) -- GitLab From 012458309b9a3b63ac1d5734500ec98c0e6d9c80 Mon Sep 17 00:00:00 2001 From: Nils Christian Date: Wed, 4 Mar 2015 22:31:41 +0100 Subject: [PATCH 0142/1172] XML::Twig for goolf 1.4.10 --- ...ML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb | 24 +++++++++++++++++++ .../XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..5248d49efa --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.41' + +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': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..acd24ee883 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Twig' +version = '3.48' + +homepage = 'http://search.cpan.org/~mirod/XML-Twig-3.48/' +description = """XML::Twig is (yet another!) XML transformation module.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('XML-Parser', '2.41', versionsuffix) +] + +options = {'modulename': 'XML::Twig'} + +moduleclass = 'data' -- GitLab From de9694f5a464b9e3e16145425daa870f7cc8de5b Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 5 Mar 2015 09:27:26 -0500 Subject: [PATCH 0143/1172] changed to BITBUCKET_SOURCE per note by @wpoely86 --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 a2767dc205..9cca953ebc 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 @@ -8,7 +8,7 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] moduleclass = 'math' -- GitLab From e7f948cf7bdee92d2d918ea7d3c2195e1b3249b7 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 14 Mar 2015 23:32:33 +0100 Subject: [PATCH 0144/1172] tophat-2.0.13 and patch --- .../t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 36 +++++++++++++++++++ .../t/TopHat/tophat-2.0.13-zlib.patch | 12 +++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb new file mode 100644 index 0000000000..f8a43fe7d6 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.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 = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.13' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-2.0.13-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0', '-Python-2.7.9'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch new file mode 100644 index 0000000000..278b2edf59 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-03-14 23:21:04.221640935 +0100 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o -- GitLab From ebab3de9e7ba5398d007785454f81bb9251f2b07 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:53:53 +0100 Subject: [PATCH 0145/1172] added boost dependency --- .../Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb new file mode 100644 index 0000000000..ce2432d59b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +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 0c2ba7ec4545445d0ecf5beba4bbaee764dffc63 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:55:00 +0100 Subject: [PATCH 0146/1172] added zlib dependency --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb new file mode 100644 index 0000000000..57a9f3a015 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.7.20'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) + toolchainopts = {'optarch': True, 'pic': True} + + sources = [SOURCELOWER_TAR_GZ] + source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +#preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' + -- GitLab From 44caa0a9e21736c8d56f8ff630b6a8de39347d5f Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:59:49 +0100 Subject: [PATCH 0147/1172] switched to used boost without python --- ....7.20-Python-2.7.9.eb => Boost-1.55.0-goolf-1.7.20.eb} | 8 ++------ .../easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 2 +- 2 files changed, 3 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/b/Boost/{Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb => Boost-1.55.0-goolf-1.7.20.eb} (76%) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb similarity index 76% rename from easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb rename to easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index ce2432d59b..269ffc6285 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -10,13 +10,9 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -pythonversion = '2.7.9' -versionsuffix = '-Python-%s' % pythonversion +configopts = '--without-libraries=python' -dependencies = [ - ('bzip2', '1.0.6'), - ('Python', pythonversion), -] +dependencies = [('bzip2', '1.0.6')] # also build boost_mpi boost_mpi = True diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index f8a43fe7d6..be9db35399 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -20,7 +20,7 @@ source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ - ('Boost', '1.55.0', '-Python-2.7.9'), + ('Boost', '1.55.0'), ('zlib', '1.2.8'), ] -- GitLab From 2f8b6e3aa86c55c605a51dcbe8cfbf78d626ad1e Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 10:03:28 +0100 Subject: [PATCH 0148/1172] style fixes zlib easyconfig --- .../easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 57a9f3a015..f87254ac39 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -6,14 +6,13 @@ 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': 'goolf', 'version': '1.7.20'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) - toolchainopts = {'optarch': True, 'pic': True} + computer hardware and operating system.""" - sources = [SOURCELOWER_TAR_GZ] - source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} -#preconfigopts = 'LDSHARED="$CC -shared"' +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], -- GitLab From 1c8dd2e257ade139800448a9c1a1611d3cf62d83 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 22:01:59 +0100 Subject: [PATCH 0149/1172] mutect easyconfig --- .../m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb diff --git a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb new file mode 100644 index 0000000000..ee2805d464 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'muTect' +version = '1.1.4' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['%(name)s-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_76' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/%(name)s-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 40f62be55263a83e33f29f37904f9031adc3923c Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:54:38 +0100 Subject: [PATCH 0150/1172] dropped empty line zlib easyconfig --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index f87254ac39..259095c5c8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -20,4 +20,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -- GitLab From 3ba64da2cf11bf579631b5ff790816026cc56a12 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:55:07 +0100 Subject: [PATCH 0151/1172] four spaces indent --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 259095c5c8..f37bbd9742 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -15,8 +15,8 @@ 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.so'], - 'dirs': [], + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], } moduleclass = 'lib' -- GitLab From 61178487b83d54b24718d290126447344aaf7a5a Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:55:36 +0100 Subject: [PATCH 0152/1172] move parallel=1 above sanity check --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index be9db35399..2a4b09be4d 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -26,11 +26,11 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST' +parallel = 1 + sanity_check_paths = { 'files': ['bin/tophat'], 'dirs': [], } -parallel = 1 - moduleclass = 'bio' -- GitLab From f42eb31af827ec056d6693d0f6333da1fc9c9c60 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:56:05 +0100 Subject: [PATCH 0153/1172] dropped empty line boost easyconfig --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 269ffc6285..72d076e794 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -20,4 +20,3 @@ boost_mpi = True osdependencies = [('zlib-devel','zlib1g-dev')] moduleclass = 'devel' - -- GitLab From 07d0e0b3b3e7d9c636d4833202a748ea6e09d53a Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:57:04 +0100 Subject: [PATCH 0154/1172] style fixes boost easyconfig --- .../easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 72d076e794..fa03c1c2ae 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -7,16 +7,16 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] - -configopts = '--without-libraries=python' +source_urls = [SOURCEFORGE_SOURCE] dependencies = [('bzip2', '1.0.6')] +osdependencies = [('zlib-devel','zlib1g-dev')] + # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +configopts = '--without-libraries=python' moduleclass = 'devel' -- GitLab From 239a018070073f89c3b171b50e709b6531906e38 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:58:51 +0100 Subject: [PATCH 0155/1172] added missing bzip2 dependency --- .../b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..718daa2bc0 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.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': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bzip.org/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'tools' -- GitLab From 1b1d525125a974ab20a9bca02a4117cb20d5fb7e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 09:30:47 +0100 Subject: [PATCH 0156/1172] Dummy --- easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From 680423817c7562b0883fc2809b7cf47ad453aab0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 11:24:07 +0100 Subject: [PATCH 0157/1172] GLPK 4.55 intel-foss 2015a --- .../g/GLPK/GLPK-4.55-foss-2015a.eb | 28 +++++++++++++++++++ .../g/GLPK/GLPK-4.55-intel-2015a.eb | 28 +++++++++++++++++++ .../g/gplk/GPLK-4.55-intel-2015a.eb | 1 - 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb new file mode 100644 index 0000000000..00491cc9ba --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +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' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..77009b52a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +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' diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb deleted file mode 100644 index 421376db9e..0000000000 --- a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb +++ /dev/null @@ -1 +0,0 @@ -dummy -- GitLab From c696dbe4d68d5d2fafd6c2547caa5c9bbf33e281 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 24 Mar 2015 16:47:08 +0100 Subject: [PATCH 0158/1172] Create BuildEnv-1.0-intel-2015a-default.eb Add an easyconfig for the BuildEnv easyblock --- .../b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb new file mode 100644 index 0000000000..7c00f91195 --- /dev/null +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -0,0 +1,13 @@ +easyblock = "BuildEnv" + +name = 'BuildEnv' +version = '1.0' +versionsuffix = '-default' + + +homepage = 'None' +description = """This module sets a set of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' -- GitLab From afb53d7ffad5c88ee04c60c75d81c2988494754c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 08:18:44 +0100 Subject: [PATCH 0159/1172] Update BuildEnv-1.0-intel-2015a-default.eb --- .../b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index 7c00f91195..93fc3fedab 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -4,9 +4,10 @@ name = 'BuildEnv' version = '1.0' versionsuffix = '-default' - homepage = 'None' -description = """This module sets a set of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software.""" +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you + can use to easily transition between toolchains when building your software. To query the variables being set please use: + module show """ toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 7e72cb4dabf6ba7af5e2d448647458eb3fbdba86 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 10:52:08 +0100 Subject: [PATCH 0160/1172] Update BuildEnv-1.0-intel-2015a-default.eb --- .../easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index 93fc3fedab..e3707468df 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -2,7 +2,6 @@ easyblock = "BuildEnv" name = 'BuildEnv' version = '1.0' -versionsuffix = '-default' homepage = 'None' description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you -- GitLab From 8f6c9de75ba19f8edf52f692dcc07f6f48dcca0f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:42:24 +0100 Subject: [PATCH 0161/1172] Update BuildEnv-1.0-intel-2015a-default.eb ```default``` is not allowed by lmod so had to use ```defaults``` --- .../easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index e3707468df..7e91b365f2 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -1,7 +1,7 @@ easyblock = "BuildEnv" name = 'BuildEnv' -version = '1.0' +version = 'defaults' homepage = 'None' description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you -- GitLab From 5bbbbf1169ff2bab36eee2d690d24584d0561e55 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:54:46 +0100 Subject: [PATCH 0162/1172] Rename BuildEnv-1.0-intel-2015a-default.eb to BuildEnv-defaults-intel-2015a-default.eb --- ...-2015a-default.eb => BuildEnv-defaults-intel-2015a-default.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/BuildEnv/{BuildEnv-1.0-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a-default.eb} (100%) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb similarity index 100% rename from easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb rename to easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb -- GitLab From e33c0ceb779e8d4fa1315f583e0b0dfc7d3bc526 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:55:05 +0100 Subject: [PATCH 0163/1172] Rename BuildEnv-defaults-intel-2015a-default.eb to BuildEnv-defaults-intel-2015a.eb --- ...ts-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/BuildEnv/{BuildEnv-defaults-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb rename to easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb -- GitLab From d31e2766fa8c2ddce8d0102126ed46833424ba8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Mar 2015 12:59:48 +0200 Subject: [PATCH 0164/1172] add easyconfig for extra R extensions that require additional dependencies --- .../c/cURL/cURL-7.41.0-intel-2015a.eb | 30 ++++++ .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 +++++ .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 99 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++ .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 +++++ 5 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb new file mode 100644 index 0000000000..7c9526c34b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.41.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# dependencies = [('OpenSSL', '1.0.1m')] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000..ba650f6541 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +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': 'intel', 'version': '2015a'} +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/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000..7ec2e95168 --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -0,0 +1,99 @@ +easyblock = 'Bundle' + +name = 'R-extra' +version = '20150323' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4'), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('RCurl', '1.95-4.5', ext_options), # requires cURL + ('XML', '3.98-1.1', ext_options), # requires libxml2 + # extensions below requires one or more extensions that have an external dependency listed above + ('picante', '1.6-2', ext_options), + ('spacodiR', '0.13.0115', ext_options), + ('picante', '1.6-2', ext_options), + ('httr', '0.6.1', ext_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('rtracklayer', '1.26.2', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('GenomicFeatures', '1.18.4', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGprofile', '1.8.0', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('Gviz', '1.10.10', bioconductor_options), + ('methyAnalysis', '1.8.0', bioconductor_options), + ('pathview', '1.6.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('spliceR', '1.8.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.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': '2015a'} + +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-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..de684154a7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb @@ -0,0 +1,24 @@ +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': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 28055f077a0cf978acf61e7ee0b7eeeb62e09dd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 12:13:27 +0200 Subject: [PATCH 0165/1172] {bio}[intel/2015a] AFNI 20141023 (WIP) --- .../a/AFNI/AFNI-20150327-intel-2015a.eb | 46 +++++++++++++++++++ .../libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb | 26 +++++++++++ .../l/libXpm/libXpm-3.5.11-intel-2015a.eb | 22 +++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb new file mode 100644 index 0000000000..a49615c9ce --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'AFNI' +version = '20141023' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +# download afni_src.tgz manually from http://afni.nimh.nih.gov/pub/dist/tgz/, and rename to include datestamp +# detailed release notes are available at http://afni.nimh.nih.gov/pub/dist/doc/misc/history/afni_hist_level1_all.html +# but last update doesn't match datestamp of most recent afni_src.tgz? +sources = ['afni_src-%(version)s.tgz'] +checksums = ['87d8fcea9b9214dd37f5d89d61605647'] + +libx11suff = '-libX11-1.6.3' + +pyver = '2.7.9' +majpyver = '.'.join(pyver.split('.')[:2]) +dependencies = [ + ('tcsh', '6.18.01'), + ('libXp', '1.0.3'), + ('libXt', '1.1.4', libx11suff), + ('libXpm', '3.5.11'), + ('libXmu', '1.1.2', libx11suff), + ('motif', '2.3.4', libx11suff), + ('R', '3.1.3'), + ('PyQt', '4.11.3', '-Python-%s' % pyver), + ('expat', '2.1.0'), + ('libpng', '1.6.16'), + ('libjpeg-turbo', '1.4.0'), +] + +buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s"' % majpyver + +files_to_copy = [(['afni'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/afni'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..083f86b1a3 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' +versionsuffix = '-libX11-1.6.3' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.4', versionsuffix), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.eb new file mode 100644 index 0000000000..69fda1c84a --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.so']], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 56a0b42c00ac2cbe1ea2239b1fe6c943da83f76d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Apr 2015 13:33:43 +0200 Subject: [PATCH 0166/1172] fix filename, flesh out buildopts for AFNI easyconfig --- ...-2015a.eb => AFNI-20141023-intel-2015a.eb} | 16 +++++++-- ...NI-20141023_omp-pragma-statement-fix.patch | 36 +++++++++++++++++++ 2 files changed, 50 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/AFNI/{AFNI-20150327-intel-2015a.eb => AFNI-20141023-intel-2015a.eb} (63%) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb similarity index 63% rename from easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb rename to easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb index a49615c9ce..bff0aa115f 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150327-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb @@ -8,7 +8,7 @@ description = """AFNI is a set of C programs for processing, analyzing, and disp a technique for mapping human brain activity.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'pic': True} # download afni_src.tgz manually from http://afni.nimh.nih.gov/pub/dist/tgz/, and rename to include datestamp # detailed release notes are available at http://afni.nimh.nih.gov/pub/dist/doc/misc/history/afni_hist_level1_all.html @@ -16,6 +16,8 @@ toolchainopts = {'openmp': True} sources = ['afni_src-%(version)s.tgz'] checksums = ['87d8fcea9b9214dd37f5d89d61605647'] +patches = ['AFNI-%(version)s_omp-pragma-statement-fix.patch'] + libx11suff = '-libX11-1.6.3' pyver = '2.7.9' @@ -34,7 +36,17 @@ dependencies = [ ('libjpeg-turbo', '1.4.0'), ] -buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s"' % majpyver +buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver +buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'LD="${CC} \$(CPROF)" ' +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver + +parallel = 1 files_to_copy = [(['afni'], 'bin')] diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch b/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch new file mode 100644 index 0000000000..7f3c8a8c07 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch @@ -0,0 +1,36 @@ +diff -ru afni_src.orig/thd_dset_to_vectim.c afni_src/thd_dset_to_vectim.c +--- afni_src.orig/thd_dset_to_vectim.c 2015-04-02 02:35:57.000000000 +0200 ++++ afni_src/thd_dset_to_vectim.c 2015-04-03 17:08:33.340433024 +0200 +@@ -74,8 +74,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -296,8 +297,9 @@ + + if( nvals < DSET_NVALS(dset) ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; ++ var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -463,8 +465,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + mmmt = mmmv[0]; + for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){ + if( mmmt[iv] == 0 ) continue ; -- GitLab From 838b269bf30cdb61ccdc69e7a6ef3deed8995455 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 9 Apr 2015 12:59:00 +0200 Subject: [PATCH 0167/1172] Added GDAL-1.9.2-goolf-1.5.16 and zlib-1.2.8 dependency --- .../g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb | 24 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-goolf-1.5.16.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..14deb76474 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '1.9.2' + +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': 'goolf', 'version': '1.5.16'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb new file mode 100644 index 0000000000..9b56c2bffb --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.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': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 70f461af0c36d24eeedc3cdb28215d186b26cd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:56:32 +0200 Subject: [PATCH 0168/1172] {chem}[intel/2015a] ABINIT 7.11.6 + libxc 2.2.2 (WIP) --- .../a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 29 +++++++++++++++++ .../l/libxc/libxc-2.2.2-intel-2015a.eb | 32 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb new file mode 100644 index 0000000000..e5ab48448f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.11.6' + +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': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' +configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000..25c12f798e --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.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': '2015a'} +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.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 61a46b5f548f4b7ebfb0e3b862b42a0f272f4f5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 14:12:50 +0200 Subject: [PATCH 0169/1172] add GSL and Glib dependencies for AFNI, also redefine XLIBS option for make build command --- .../a/AFNI/AFNI-20141023-intel-2015a.eb | 3 +++ .../g/GLib/GLib-2.44.0-GCC-4.9.2.eb | 23 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb index bff0aa115f..94ac7b95ff 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb @@ -34,6 +34,8 @@ dependencies = [ ('expat', '2.1.0'), ('libpng', '1.6.16'), ('libjpeg-turbo', '1.4.0'), + ('GSL', '1.16'), + ('GLib', '2.44.0', '', ('GCC', '4.9.2')), ] buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver @@ -45,6 +47,7 @@ buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'LD="${CC} \$(CPROF)" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver +buildopts += 'XLIBS="-lXm -lXt"' parallel = 1 diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..08bf6bb8cb --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.44.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9', '-bare')] + +modextrapaths = {'CPATH': ['include/glib-2.0', 'lib/glib-2.0/include']} + +moduleclass = 'vis' -- GitLab From 69f4fa55234443c3d9f2a7dbeb4f6453c4cd919a Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:40:57 +0200 Subject: [PATCH 0170/1172] R-3.2.0-goolf-1.7.20.eb --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 430 ++++++++++++++++++ 1 file changed, 430 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..a46bee15ff --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -0,0 +1,430 @@ +name = 'R' +version = '3.2.0' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', 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('data.table', '1.9.4', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-40', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.9', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), # requires R-3.1.1 or higher + ('affyio', '1.34.0', bioconductor_options), + ('BiocInstaller', '1.16.2', bioconductor_options), + ('preprocessCore', '1.28.0', bioconductor_options), + ('affy', '1.44.0', bioconductor_options), + ('GO.db', '3.0.0', bioconductor_options), + ('limma', '3.22.7', bioconductor_options), + ('RBGL', '1.42.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.7', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('XML', '3.98-1.1', ext_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('httr', '0.6.1', ext_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('widgetTools', '1.44.0', bioconductor_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('maptools', '0.8-34', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-0', ext_options), + ('goftest', '1.0-2', ext_options), + ('spatstat', '1.41-1', ext_options), + ('rgeos', '0.3-8', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('bio3d', '2.2-2', ext_options), + +] + +moduleclass = 'lang' -- GitLab From 9061990415ce599048a4c0954d7104b28ec77092 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:41:36 +0200 Subject: [PATCH 0171/1172] switched to java-1.7.0_80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index a46bee15ff..47aa361cd5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] name_tmpl = '%(name)s_%(version)s.tar.gz' -- GitLab From edc13f8789fe70056b384b350618bdabca4a7bdf Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:56:40 +0200 Subject: [PATCH 0172/1172] libs updated 26-04-2015 --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 196 +++++++++--------- 1 file changed, 98 insertions(+), 98 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 47aa361cd5..3087ff6e51 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -73,21 +73,21 @@ exts_list = [ ('combinat', '0.0-8', ext_options), ('deal', '1.2-37', ext_options), ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.1', ext_options), + ('formatR', '1.2', ext_options), ('gtools', '3.4.2', ext_options), ('gdata', '2.13.3', ext_options), ('GSA', '1.03', ext_options), - ('highr', '0.4.1', ext_options), + ('highr', '0.5', ext_options), ('infotheo', '1.2.0', ext_options), ('lars', '1.2', ext_options), ('lazy', '1.2-15', ext_options), ('kernlab', '0.9-20', ext_options), ('mime', '0.3', ext_options), - ('markdown', '0.7.4', ext_options), + ('markdown', '0.7.7', ext_options), ('mlbench', '2.1-1', ext_options), ('NLP', '0.1-6', ext_options), - ('mclust', '5.0.0', ext_options), - ('RANN', '2.4.1', ext_options), + ('mclust', '5.0.1', ext_options), + ('RANN', '2.5', ext_options), ('rmeta', '2.16', ext_options), ('segmented', '0.5-1.1', ext_options), ('som', '0.3-5', ext_options), @@ -119,7 +119,7 @@ exts_list = [ ('spam', '1.0-1', ext_options), ('subplex', '1.1-4', ext_options), ('stringr', '0.6.2', ext_options), - ('evaluate', '0.6', ext_options), + ('evaluate', '0.7', ext_options), ('logspline', '2.1.5', ext_options), ('ncbit', '2013.03.29', ext_options), ('permute', '0.8-3', ext_options), @@ -136,8 +136,8 @@ exts_list = [ ('Matrix', '1.2-0', ext_options), ('png', '0.1-7', ext_options), ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), + ('RcppArmadillo', '0.5.000.0', ext_options), + ('plyr', '1.8.2', ext_options), ('pROC', '1.7.3', ext_options), ('quadprog', '1.5-5', ext_options), ('BB', '2014.10-1', ext_options), @@ -158,7 +158,7 @@ exts_list = [ ('mgcv', '1.8-6', ext_options), ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), + ('sp', '1.1-0', ext_options), ('vcd', '1.3-2', ext_options), ('snowfall', '1.84-6', ext_options), ('rpart', '4.1-9', ext_options), @@ -169,7 +169,7 @@ exts_list = [ ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), + ('mixtools', '1.0.3', ext_options), ('cluster', '2.0.1', ext_options), ('gclus', '1.3.1', ext_options), ('coda', '0.17-1', ext_options), @@ -213,23 +213,23 @@ exts_list = [ ('R.methodsS3', '1.7.0', ext_options), ('R.oo', '1.19.0', ext_options), ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), + ('R.utils', '2.0.1', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.12.1', bioconductor_options), - ('Biobase', '2.26.0', bioconductor_options), - ('S4Vectors', '0.4.0', bioconductor_options), - ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.5', bioconductor_options), - ('AnnotationDbi', '1.28.2', bioconductor_options), - ('XVector', '0.6.0', bioconductor_options), - ('zlibbioc', '1.12.0', bioconductor_options), - ('Biostrings', '2.34.1', bioconductor_options), - ('GenomicRanges', '1.18.4', bioconductor_options), - ('Rsamtools', '1.18.3', bioconductor_options), - ('BiocParallel', '1.0.3', bioconductor_options), - ('GenomicAlignments', '1.2.2', bioconductor_options), - ('ShortRead', '1.24.0', bioconductor_options), - ('graph', '1.44.1', bioconductor_options), + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.0', bioconductor_options), + ('IRanges', '2.2.1', bioconductor_options), + ('GenomeInfoDb', '1.4.0', bioconductor_options), + ('AnnotationDbi', '1.30.0', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.0', bioconductor_options), + ('GenomicRanges', '1.20.3', bioconductor_options), + ('Rsamtools', '1.20.1', bioconductor_options), + ('BiocParallel', '1.2.0', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), ('Formula', '1.2-1', ext_options), @@ -277,7 +277,7 @@ exts_list = [ ('glmnet', '2.0-2', ext_options), ('labdsv', '1.6-1', ext_options), ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), + ('stabs', '0.5-1', ext_options), ('mboost', '2.4-2', ext_options), ('msm', '1.5', ext_options), ('nor1mix', '1.2-0', ext_options), @@ -296,7 +296,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), + ('knitr', '1.10', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), ('maxLik', '1.2-4', ext_options), @@ -306,33 +306,33 @@ exts_list = [ ('reshape', '0.8.5', ext_options), ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), # requires R-3.1.1 or higher - ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), - ('preprocessCore', '1.28.0', bioconductor_options), - ('affy', '1.44.0', bioconductor_options), - ('GO.db', '3.0.0', bioconductor_options), - ('limma', '3.22.7', bioconductor_options), - ('RBGL', '1.42.0', bioconductor_options), - ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.2', bioconductor_options), - ('KEGG.db', '3.0.0', bioconductor_options), - ('annaffy', '1.38.0', bioconductor_options), - ('gcrma', '2.38.0', bioconductor_options), - ('oligoClasses', '1.28.0', bioconductor_options), - ('edgeR', '3.8.6', bioconductor_options), - ('PFAM.db', '3.0.0', bioconductor_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.1', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.0', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.1', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.0', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.0', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), - ('baySeq', '2.0.50', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), - ('qvalue', '1.43.0', bioconductor_options), - ('impute', '1.40.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), ('matrixStats', '0.14.0', ext_options), ('samr', '2.0', ext_options), - ('DEGseq', '1.20.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), @@ -345,76 +345,76 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('hgu133plus2.db', '3.1.2', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('illuminaio', '0.8.0', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), ('registry', '0.2', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), - ('bumphunter', '1.6.0', bioconductor_options), - ('multtest', '2.22.0', bioconductor_options), - ('siggenes', '1.40.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), ('nleqslv', '2.7', ext_options), - ('DynDoc', '1.44.0', bioconductor_options), - ('genoset', '1.20.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.8.0', bioconductor_options), + ('NOISeq', '2.10.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), - ('Rgraphviz', '2.10.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), - ('RNASeqPower', '1.6.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), - ('biomaRt', '2.22.0', bioconductor_options), - ('annotate', '1.44.0', bioconductor_options), - ('GSEABase', '1.28.0', bioconductor_options), - ('genefilter', '1.48.1', bioconductor_options), - ('Category', '2.32.0', bioconductor_options), - ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.2', bioconductor_options), - ('GOstats', '2.32.0', bioconductor_options), - ('rtracklayer', '1.26.3', bioconductor_options), - ('GenomicFeatures', '1.18.7', bioconductor_options), - ('BSgenome', '1.34.1', bioconductor_options), - ('VariantAnnotation', '1.12.9', bioconductor_options), - ('biovizBase', '1.14.1', bioconductor_options), - ('OrganismDbi', '1.8.1', bioconductor_options), - ('ggbio', '1.14.0', bioconductor_options), - ('geneplotter', '1.44.0', bioconductor_options), - ('DESeq2', '1.6.3', bioconductor_options), - ('ReportingTools', '2.6.0', bioconductor_options), - ('genefilter', '1.48.1', bioconductor_options), - ('affycoretools', '1.38.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.0', bioconductor_options), + ('GSEABase', '1.30.1', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.0', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.2', bioconductor_options), + ('GenomicFeatures', '1.20.0', bioconductor_options), + ('BSgenome', '1.36.0', bioconductor_options), + ('VariantAnnotation', '1.14.0', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.0', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('affycoretools', '1.40.1', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), ('Homo.sapiens', '1.1.2', bioconductor_options), ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.16.0', bioconductor_options), - ('GenomeGraphs', '1.26.0', bioconductor_options), - ('geneLenDataBase', '1.1.1', bioconductor_options), - ('goseq', '1.18.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), ('httr', '0.6.1', ext_options), - ('KEGGREST', '1.6.4', bioconductor_options), - ('KEGGgraph', '1.24.0', bioconductor_options), - ('KEGGprofile', '1.8.2', bioconductor_options), - ('minfi', '1.12.0', bioconductor_options), - ('methylumi', '2.12.0', bioconductor_options), - ('lumi', '2.18.0', bioconductor_options), - ('widgetTools', '1.44.0', bioconductor_options), - ('tkWidgets', '1.44.0', bioconductor_options), - ('Mfuzz', '2.26.0', bioconductor_options), - ('maSigPro', '1.38.0', bioconductor_options), - ('SPIA', '2.18.0', bioconductor_options), - ('Gviz', '1.10.11', bioconductor_options), - ('cummeRbund', '2.8.2', bioconductor_options), - ('maptools', '0.8-34', ext_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.1', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.0', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), ('tensor', '1.5', ext_options), ('polyclip', '1.3-0', ext_options), -- GitLab From f557d3632c2e91a1994df55434463f61f1cf4b83 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Mon, 27 Apr 2015 11:08:19 +0200 Subject: [PATCH 0173/1172] updated to latest libpng --- .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb new file mode 100644 index 0000000000..8e90204af6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 3087ff6e51..93ecdc515d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] -- GitLab From 988a11260662f2b1b7bea3aca07847272cc56535 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Mon, 27 Apr 2015 11:14:38 +0200 Subject: [PATCH 0174/1172] removed libpng easyconfig which is already in develop --- .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb deleted file mode 100644 index 8e90204af6..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.17' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' -description = "libpng is the official PNG reference library" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -moduleclass = 'lib' -- GitLab From 2b2dcd9e93940f02ad86d23d851fcdd74d65e6b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 10:54:06 +0200 Subject: [PATCH 0175/1172] include patch for Python 2.5.6 to fix issue with newer versions of 'svnversion' command that spits out 'Unversioned directory' rather than 'exported' --- .../Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 ++ .../Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 ++ .../p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 ++ .../p/Python/Python-2.5.6_svnversion-cmd.patch | 12 ++++++++++++ 8 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index a0f450f70f..43ff3feba7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 53b6064132..f825fd87bd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ed1944c3f2..18d0d4a8df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index d9118da106..5cad1244b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + patches = ['python_libffi_int128_icc.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index da9bd1c2a4..eecf1e2276 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + patches = ['python_libffi_int128_icc.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index ae0e9d0e08..0228eae5be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index 6d976f526f..fc44c37e78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch new file mode 100644 index 0000000000..eef94268d9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -0,0 +1,12 @@ +--- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 ++++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 +@@ -4242,7 +4242,8 @@ + + if test $SVNVERSION = found + then +- SVNVERSION="svnversion \$(srcdir)" ++ #SVNVERSION="svnversion \$(srcdir)" ++ SVNVERSION="echo exported" + else + SVNVERSION="echo exported" + fi -- GitLab From 454e95a3227952c3e1d4743bf5882af4644e303e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:25:43 +0200 Subject: [PATCH 0176/1172] dummy --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 995c8f51d24a0ee8950f96471e01d87b18d54226 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:34:10 +0200 Subject: [PATCH 0177/1172] HMMER 3.1b2 with intel-2015a --- .../h/HMMER/HMMER-3.1b2-intel-2015a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index e69de29bb2..5255f85ddc 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , 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 = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.janelia.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", + "esl-alimap", "esl-cluster", "esl-mask"]], + 'dirs': [] +} + +runtest = 'check' + +moduleclass = 'bio' -- GitLab From e0027ca8d8c3107c6588145867e4532484017d25 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 30 Apr 2015 08:56:53 +0200 Subject: [PATCH 0178/1172] Dummy --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 89f4e4170a0685beececd12fc9bf083377ade19e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 30 Apr 2015 09:53:25 +0200 Subject: [PATCH 0179/1172] eudev 1st try --- .../e/eudev/eudev-3.0-intel-2014b.eb | 31 +++++++++++++++++++ .../e/eudev/eudev-3.0_pre-2.6.34_kernel.patch | 16 ++++++++++ .../g/gperf/gperf-3.0.4-intel-2014b.eb | 23 ++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index e69de29bb2..b64ac043f3 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2014b'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +preinstallopts = "make 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/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch new file mode 100644 index 0000000000..7fb7da7902 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch @@ -0,0 +1,16 @@ +#inspiration from http://repository.timesys.com/buildsources/u/udev/udev-181/udev-181-define-trigger-happy.patch +#BTN_TRIGGER_HAPPY is not defined in /usr/include/linux/input.h for pre 2.6.34 kernels +# B. Hajgato April 30 2015 +--- eudev-3.0/src/udev/udev-builtin-input_id.c.org 2015-04-30 09:11:07.990269206 +0200 ++++ eudev-3.0/src/udev/udev-builtin-input_id.c 2015-04-30 09:12:19.407272116 +0200 +@@ -33,6 +33,10 @@ + #include "udev.h" + #include "util.h" + ++#ifndef BTN_TRIGGER_HAPPY ++#define BTN_TRIGGER_HAPPY 0x2c0 ++#endif ++ + /* we must use this kernel-compatible implementation */ + #define BITS_PER_LONG (sizeof(unsigned long) * 8) + #define NBITS(x) ((((x)-1)/BITS_PER_LONG)+1) diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb new file mode 100644 index 0000000000..bef0d843d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb @@ -0,0 +1,23 @@ +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': 'intel', 'version': '2014b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] + } + +moduleclass = 'devel' -- GitLab From 64389a02f3dfaec9bf1cb98ea088df5d96e98d36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2015 00:34:47 +0300 Subject: [PATCH 0180/1172] {geo}[foss/2015a] WRF 3.6.1 --- .../b/Bison/Bison-3.0.2-foss-2015a.eb | 22 ++++++++++ .../c/CMake/CMake-3.0.0-foss-2015a.eb | 22 ++++++++++ .../c/cURL/cURL-7.37.1-foss-2015a.eb | 27 +++++++++++++ .../d/Doxygen/Doxygen-1.8.7-foss-2015a.eb | 18 +++++++++ .../f/flex/flex-2.5.39-foss-2015a.eb | 14 +++++++ .../h/HDF5/HDF5-1.8.13-foss-2015a.eb | 25 ++++++++++++ .../j/JasPer/JasPer-1.900.1-foss-2015a.eb | 21 ++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 23 +++++++++++ .../netCDF-Fortran-4.4.0-foss-2015a.eb | 17 ++++++++ .../n/netCDF/netCDF-4.3.2-foss-2015a.eb | 31 ++++++++++++++ .../t/tcsh/tcsh-6.18.01-foss-2015a.eb | 38 ++++++++++++++++++ .../w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb | 40 +++++++++++++++++++ 12 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb new file mode 100644 index 0000000000..0b270e9381 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'foss', 'version': '2015a'} + +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-3.0.0-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb new file mode 100644 index 0000000000..c55a48656c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': 'foss', 'version': '2015a'} + +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' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb new file mode 100644 index 0000000000..0ba45ba9e5 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb new file mode 100644 index 0000000000..6fae2382dd --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb new file mode 100644 index 0000000000..f9226ff5f3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.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': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb new file mode 100644 index 0000000000..f79d365b61 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2015a'} +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 = [ + '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/j/JasPer/JasPer-1.900.1-foss-2015a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb new file mode 100644 index 0000000000..02cb1d4f4c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.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': 'foss', 'version': '2015a'} +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' 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 new file mode 100644 index 0000000000..411820a76b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.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': 'foss', 'version': '2015a'} + +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/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb new file mode 100644 index 0000000000..d623122642 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +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': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000..8319de8066 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -0,0 +1,31 @@ +name = 'netCDF' +version = '4.3.2' + +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': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb new file mode 100644 index 0000000000..4b5f7237ff --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.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 = '6.18.01' + +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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb new file mode 100644 index 0000000000..5e773ca4e8 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WRF' +version = '3.6.1' + +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': 'foss', 'version': '2015a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)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', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_netCDF-Fortran_separate_path.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' -- GitLab From 6ac754ac68b4e5db51fbff7dadcb589ce4de04cd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 5 May 2015 11:58:22 +0200 Subject: [PATCH 0181/1172] CGAL version bump --- .../CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 31 +++++++++++++++++++ .../g/GLib/GLib-2.44.0-intel-2015a.eb | 21 +++++++++++++ .../g/gettext/gettext-0.19.4-intel-2015a.eb | 18 +++++++++++ .../l/libffi/libffi-3.2.1-intel-2015a.eb | 23 ++++++++++++++ .../MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb | 30 ++++++++++++++++++ .../q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb | 23 ++++++++++++++ 6 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bb0ac3e82d --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] +# The directory changes with the version (and maybe in time) ---^ +# Have to accept license agreement + +pythonversion = '2.7.9' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a'), + ('Boost', '1.57.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddeps = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' + diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb new file mode 100644 index 0000000000..345c9887e6 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.44.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb new file mode 100644 index 0000000000..0dbf6fce3a --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000..385b07e0ea --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.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': 'intel', 'version': '2015a'} + +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/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb new file mode 100644 index 0000000000..147f24acc7 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.2' + +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': '2015a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +gmp='GMP' +gmpver='6.0.0a' +versionsuffix='-%s-%s' % (gmp,gmpver) + +dependencies = [(gmp, gmpver)] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb new file mode 100644 index 0000000000..0b1ba51db0 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb @@ -0,0 +1,23 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-4.8.6_icc-qUnused.patch'] + +glib='GLib' +glibver='2.44.0' +versionsuffix="-%s-%s" % (glib,glibver) + +dependencies = [(glib, glibver)] + +moduleclass = 'devel' -- GitLab From d30c3bb38f9bc53bd6f1145854607c759ccf0ac7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 May 2015 10:23:17 +0200 Subject: [PATCH 0182/1172] Minor corrections --- easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb index bef0d843d8..d44084ea5c 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb @@ -9,15 +9,14 @@ description = """GNU gperf is a perfect hash function generator. For a given lis 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': 'intel', 'version': '2014b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' -- GitLab From 94a3c2c5d41a25185b234b6545b23f09ba91088c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 May 2015 11:31:39 +0200 Subject: [PATCH 0183/1172] Boost 1.57 -> 1.58 --- .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index bb0ac3e82d..374c22547b 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -18,7 +18,7 @@ versionsuffix = "-Python-%s" % pythonversion dependencies = [ ('GMP', '6.0.0a'), - ('Boost', '1.57.0', versionsuffix), + ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), ('Qt', '4.8.6', '-GLib-2.44.0'), ] -- GitLab From 9a99585aa93e4592fe8b7467b58e81adc1a15d3c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 7 May 2015 14:26:22 +0200 Subject: [PATCH 0184/1172] With foss-2015a as well --- .../CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb | 31 +++++++++++++++++++ .../g/GLib/GLib-2.44.0-foss-2015a.eb | 21 +++++++++++++ .../g/gettext/gettext-0.19.4-foss-2015a.eb | 18 +++++++++++ .../l/libffi/libffi-3.2.1-foss-2015a.eb | 23 ++++++++++++++ .../MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb | 30 ++++++++++++++++++ .../q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb | 21 +++++++++++++ 6 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1eb2d83747 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] +# The directory changes with the version (and maybe in time) ---^ +# Have to accept license agreement + +pythonversion = '2.7.9' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a'), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddeps = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' + diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb new file mode 100644 index 0000000000..209f2f13dd --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.44.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb new file mode 100644 index 0000000000..51c244d3ef --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb new file mode 100644 index 0000000000..17a9f263e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.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': '2015a'} + +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/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb new file mode 100644 index 0000000000..3ff2a17d36 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.2' + +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': '2015a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +gmp='GMP' +gmpver='6.0.0a' +versionsuffix='-%s-%s' % (gmp,gmpver) + +dependencies = [(gmp, gmpver)] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb new file mode 100644 index 0000000000..9fce73a06d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb @@ -0,0 +1,21 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +glib='GLib' +glibver='2.44.0' +versionsuffix="-%s-%s" % (glib,glibver) + +dependencies = [(glib, glibver)] + +moduleclass = 'devel' -- GitLab From 560459d37056e8ffa48567f623a9468356a76944 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 11:20:50 +0100 Subject: [PATCH 0185/1172] Add Plumed easyconfig --- .../easyconfigs/p/plumed/configure.patch | 39 +++++++++++++++++++ .../p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 34 ++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/plumed/configure.patch create mode 100644 easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb diff --git a/easybuild/easyconfigs/p/plumed/configure.patch b/easybuild/easyconfigs/p/plumed/configure.patch new file mode 100644 index 0000000000..c96081c3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/plumed/configure.patch @@ -0,0 +1,39 @@ +# patch to work around the hideous build system of plumed. We use the values +# EB sets in the build system. +diff -urN plumed-2.0.4.orig/configurations/linux.icc plumed-2.0.4/configurations/linux.icc +--- plumed-2.0.4.orig/configurations/linux.icc 2014-09-15 11:41:47.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.icc 2014-12-01 14:54:42.000000000 +0100 +@@ -2,21 +2,21 @@ + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl ++LIBS:=-ldl $(LIBS) +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=icc -shared $(CFLAGS) +-LD=icpc +-LDF90=ifort +-CXX=icpc +-CC=icc +-FC=ifort ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=g++ + diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb new file mode 100644 index 0000000000..08d824f5cf --- /dev/null +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -0,0 +1,34 @@ +# This is a quickly made easyconfig, using some dirty tricks... +# Warning: Here be dragons +# by Ward Poelmans + +name = 'plumed' +version = '2.0.4' + +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': 'ictce', 'version': '7.1.2'} + +# Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url +sources = ['plumed-2.0.4.tgz'] + +patches = ['configure.patch'] + +preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +# should probably happen in a easyblock. This vars needs to be set +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' -- GitLab From 31932b90aee480fc2f376ba3706689c5a03667c6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 12 May 2015 10:11:05 +0200 Subject: [PATCH 0186/1172] Updated plumed --- .../p/plumed/{configure.patch => configure-2.0.4.patch} | 0 easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 5 +++-- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/plumed/{configure.patch => configure-2.0.4.patch} (100%) diff --git a/easybuild/easyconfigs/p/plumed/configure.patch b/easybuild/easyconfigs/p/plumed/configure-2.0.4.patch similarity index 100% rename from easybuild/easyconfigs/p/plumed/configure.patch rename to easybuild/easyconfigs/p/plumed/configure-2.0.4.patch diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb index 08d824f5cf..b146ba0970 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -16,9 +16,10 @@ The software, written in C++, can be easily interfaced with both fortran and C/C toolchain = {'name': 'ictce', 'version': '7.1.2'} # Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url -sources = ['plumed-2.0.4.tgz'] +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v2.0.4.tar.gz'] -patches = ['configure.patch'] +patches = ['configure-%(version)s.patch'] preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " -- GitLab From 6fece1573017a6442de47ed240629d5ebbce8e67 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 12 May 2015 11:09:44 +0200 Subject: [PATCH 0187/1172] added easyblock line --- easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb index b146ba0970..3eda065ef1 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -2,6 +2,8 @@ # Warning: Here be dragons # by Ward Poelmans +easyblock = 'ConfigureMake' + name = 'plumed' version = '2.0.4' -- GitLab From 0a5a707410bc0c3fab77da9a0ee24053a53a7802 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 19 May 2015 14:04:48 +0200 Subject: [PATCH 0188/1172] os dependency added --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index b64ac043f3..3efae98cdb 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -20,6 +20,8 @@ builddependencies = [ ('gperf', '3.0.4'), ] +osdependencies = [('kernel-headers','linux-libc-dev')] + configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' preinstallopts = "make check && " -- GitLab From f538dec34e341bafb991c8288be9b88aab7215f1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 19 May 2015 14:52:04 +0200 Subject: [PATCH 0189/1172] dummy --- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 27b00c44c74ed82935e9d85181a81c98b9fb9b40 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 08:26:56 +0200 Subject: [PATCH 0190/1172] split 1 --- .../fontsproto-2.1.3-intel-2015a.eb | 20 +++++ ...bXdamage-1.1.4-intel-2015a-Python-2.7.9.eb | 26 +++++++ ...libXfont-1.5.1-intel-2015a-Python-2.7.9.eb | 30 ++++++++ .../libfontenc-1.1.3-intel-2015a.eb | 23 ++++++ .../Mesa-10.5.5-intel-2015b-Python-2.7.9.eb | 75 +++++++++++++++++++ 5 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.eb 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 new file mode 100644 index 0000000000..7e4853de2f --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.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': 'intel', 'version': '2015a'} +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/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..9934005796 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' +versionsuffix = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), + ('libxcb', '1.11', versionsuffix), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.so', 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7ed47b7b55 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' +versionsuffix = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.so', 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.eb new file mode 100644 index 0000000000..b6a5cba0db --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.so', 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb index e69de29bb2..6920abd0e9 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb @@ -0,0 +1,75 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '10.5.5' + +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': '2015a'} +toolchainopts = {'optarch': True} + +sources = ['%sLib-%s.tar.gz' % (name, version)] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('pkg-config', '0.28'), + ('libtool', '2.4.5'), + ('glproto', '1.4.17'), + ('kbproto, '1.0.6'), + ('xextproto, '7.3.0'), + ('xproto', '7.0.27'), + ('makedepend', '1.0.5'), + ('M4', '1.4.17'), ++ ('LLVM', '3.6'), + +dependencies = [ + ('Python', pythonver), + ('libxml2', '2.9.2', versionsuffix), + ('libdrm', '2.4.59'), + ('libX11', '1.6.3', versionsuffix), + ('libXext', '1.3.3'), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4', versionsuffix), + ('libXfont', '1.5.1', versionsuffix), ++ ('eudev', '3.0'), +] + +#Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --enable-osmesa --enable-gallium --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl " + +# 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.so', '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/GL/wmesa.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' -- GitLab From 5854c953b9f93d8d38e508d64971d6b0a4d22505 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 08:29:18 +0200 Subject: [PATCH 0191/1172] with intel-2015a as well --- .../e/eudev/eudev-3.0-intel-2015a.eb | 33 +++++++++++++++++++ .../g/gperf/gperf-3.0.4-intel-2015a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb new file mode 100644 index 0000000000..9ada9135c9 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_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 ' +preinstallopts = "make 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/g/gperf/gperf-3.0.4-intel-2015a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb new file mode 100644 index 0000000000..03d48cbdf1 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.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': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From ba52e419dc712061dd493be18db73a29db5a2446 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 09:00:02 +0200 Subject: [PATCH 0192/1172] llvm-core --- easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb | 26 ++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb new file mode 100644 index 0000000000..d6bfa425d7 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb @@ -0,0 +1,26 @@ +easyblock='CMakeMake' + +name = "LLVM" +version = "3.6.0" + +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': '2015a'} +# 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"] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'compiler' -- GitLab From 5cc98ca6e5be1640031db6e41d9fe67a3ea782b5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 10:51:54 +0200 Subject: [PATCH 0193/1172] Fixes, sanity check --- easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb index d6bfa425d7..40802cfa30 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb @@ -13,14 +13,21 @@ description = """The LLVM Core libraries provide a modern source- and target-ind to use LLVM as an optimizer and code generator.""" toolchain = {'name': 'intel', 'version': '2015a'} -# Do not set optarch to True: it will cause the build to fail -toolchainopts = {'optarch': False} +toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ - ('CMake', '3.1.3'), + ('CMake', '3.2.2'), + ('Python', '2.7.9'), ] +sanity_check_paths = { + 'files' : ['bin/llvm-ar'], + 'dirs' : ['include/llvm', 'inclide/llvm-c'], +} + +separate_build_dir = True + moduleclass = 'compiler' -- GitLab From 1009235604f4daa0eb83b0dd659c66d0f8ffe7d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:06:28 +0200 Subject: [PATCH 0194/1172] add Tk without X11 support --- .../t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb 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 new file mode 100644 index 0000000000..50b6df47b2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,25 @@ +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': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 608bf4f4f79fc12b13a9195cb9b0aef95bdf2fe4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 11:07:24 +0200 Subject: [PATCH 0195/1172] Module correctly named --- .../l/LLVM/{LLVM-3.6.0.eb => LLVM-3.6.0-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/LLVM/{LLVM-3.6.0.eb => LLVM-3.6.0-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/l/LLVM/LLVM-3.6.0.eb rename to easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb -- GitLab From 206c5f6ff26612114751151767a7e9ebc9c2f220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:15:39 +0200 Subject: [PATCH 0196/1172] remove libX11 dep from no-X11 Tk easyconfig --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 - 1 file changed, 1 deletion(-) 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 50b6df47b2..39ccca9596 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 @@ -15,7 +15,6 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From becefcb5a6635e5df687e18c59313044ddddd775 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:44:22 +0200 Subject: [PATCH 0197/1172] use no-X11 Tk as dep in R-extra easyconfig --- .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 2 +- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 ------------------- .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 ------------------ 3 files changed, 1 insertion(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb index 7ec2e95168..6cd16e2bf9 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), ('Tcl', '8.6.4'), - ('Tk', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb deleted file mode 100644 index b2673863fd..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,25 +0,0 @@ -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': '2015a'} - -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-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb deleted file mode 100644 index de684154a7..0000000000 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,24 +0,0 @@ -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': 'intel', 'version': '2015a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), -] - -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' - -start_dir = 'unix' - -moduleclass = 'vis' -- GitLab From 47425566ec284aedcef88164534216baf30a3f3d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 11:46:59 +0200 Subject: [PATCH 0198/1172] LLVM is a dep not a builddep --- .../m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb index 6920abd0e9..cc91b74197 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb @@ -11,7 +11,7 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True} -sources = ['%sLib-%s.tar.gz' % (name, version)] +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', @@ -29,12 +29,12 @@ builddependencies = [ ('pkg-config', '0.28'), ('libtool', '2.4.5'), ('glproto', '1.4.17'), - ('kbproto, '1.0.6'), - ('xextproto, '7.3.0'), + ('kbproto', '1.0.6'), + ('xextproto', '7.3.0'), ('xproto', '7.0.27'), ('makedepend', '1.0.5'), ('M4', '1.4.17'), -+ ('LLVM', '3.6'), +] dependencies = [ ('Python', pythonver), @@ -45,14 +45,15 @@ dependencies = [ ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4', versionsuffix), ('libXfont', '1.5.1', versionsuffix), -+ ('eudev', '3.0'), + ('LLVM', '3.6.0'), + ('eudev', '3.0'), ] #Use the os provided libudev or the EB provided eudev #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --enable-osmesa --enable-gallium --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts = " --enable-osmesa --enable-gallium --enable-gallium-llvm --enable-glx --disable-dri --disable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl " # package-config files for os dependencies are in an os specific place -- GitLab From f0b88162888cec97df7788b437445f0f98efaa82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 12:00:37 +0200 Subject: [PATCH 0199/1172] readd Tcl 8.6.4 that is required as a dep --- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.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': '2015a'} + +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 fb8044ca44f24478cdf8eb2e066a985e2dec7a40 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 12:14:50 +0200 Subject: [PATCH 0200/1172] with shared libs --- easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb index 40802cfa30..86d25e869b 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb @@ -23,9 +23,11 @@ builddependencies = [ ('Python', '2.7.9'), ] +configopts = '-DBUILD_SHARED_LIBS=ON ' + sanity_check_paths = { 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'inclide/llvm-c'], + 'dirs' : ['include/llvm', 'include/llvm-c'], } separate_build_dir = True -- GitLab From 0d76771c5c74070fb1832a345732704244757350 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 14:09:45 +0200 Subject: [PATCH 0201/1172] Mesa with gallium OSMesa --- .../m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb index cc91b74197..cd0e005ead 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb @@ -53,8 +53,8 @@ dependencies = [ #osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --enable-osmesa --enable-gallium --enable-gallium-llvm --enable-glx --disable-dri --disable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place #preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' @@ -63,7 +63,8 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { - 'files': ['lib/libGL.so', 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'files': ['lib/libGL.so', 'libOSMesa.so', + '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', -- GitLab From b32d2bf473fbd97d13bc5ec9c07713e0dbd8a52b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 14:12:04 +0200 Subject: [PATCH 0202/1172] Sanity check path corrected --- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb index cd0e005ead..33fc721a75 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb @@ -63,7 +63,7 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { - 'files': ['lib/libGL.so', 'libOSMesa.so', + 'files': ['lib/libGL.so', 'lib/libOSMesa.so', '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', -- GitLab From 6c6c63d9e27c12d2ae6b99f88af11fbd8cf28637 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 13:41:12 +0200 Subject: [PATCH 0203/1172] WIP for R-bundles and devtools. Renaming the file and giving it a fix for the versionsuffix. Updated to reflect boegel's comment. --- ...s-20150520-intel-2015a-R-3.1.3-devtools.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb new file mode 100644 index 0000000000..cf38b2b642 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-bundles' +version = '20150520' +bundlename = 'devtools' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.3.1', ext_options), + ('roxygen2', '4.1.1', ext_options), + ('git2r', '0.10.1', ext_options), + ('RCurl', '1.95-4.6', ext_options), + ('httr', '0.6.1', ext_options), + ('rversions', '1.0.0', ext_options), + ('devtools', '1.8.0', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' + -- GitLab From afa60d29df4fe8302f4ec69816fa2cfbe8b0415f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 16:45:41 +0200 Subject: [PATCH 0204/1172] Roll back the cURL version since 7.41.0 is parked in a WIP PR. --- .../R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb index cf38b2b642..8cb259acf8 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.41.0'), + ('cURL', '7.40.0'), ('libxml2', '2.9.2'), ] -- GitLab From f2d25bea1c5399f3d5b22e2f25f915ab2adac5ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:05:19 +0200 Subject: [PATCH 0205/1172] {vis}[intel/2015a] SPIDER 22.10 --- .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 41 +++++++++++ .../SPIDER-22.10_fix-syntax-ifort.patch | 71 +++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb new file mode 100644 index 0000000000..f9744a6899 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch new file mode 100644 index 0000000000..9857ea9f14 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -0,0 +1,71 @@ +--- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 ++++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 +@@ -88,7 +88,7 @@ + INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) + INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) + +- CHARACTER(LEN=1), ALLOCATABLE :: CVAL(:) ++ CHARACTER(LEN=:), ALLOCATABLE :: CVAL + + CHARACTER(LEN=24) :: CDATE + +@@ -290,7 +290,7 @@ + IF ( ICOUNT > ICVAL_LEN) THEN + IF (ALLOCATED(CVAL)) DEALLOCATE(CVAL) + ICVAL_LEN = ICOUNT +- ALLOCATE(CVAL(1)(ICVAL_LEN), STAT=IRTFLG) ++ ALLOCATE(CHARACTER(LEN=ICVAL_LEN) :: CVAL, STAT=IRTFLG) + + IF (IRTFLG .NE. 0) THEN + CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) +@@ -432,7 +432,7 @@ + GOTRESU = .TRUE. + + ELSEIF (ITAG == 306) THEN +- CDATE = CVAL(1)(1:22) ++ CDATE = CVAL(1:22) + c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', + c & CVAL(1)(1:ICOUNT) + GOTDATE = .TRUE. +--- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 ++++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 +@@ -269,7 +269,7 @@ + ENDIF + + C GREATER OF (0 AND (THE SMALLER OF RVAL AND 255)) +- IVAL = MAX(0,MIN(RVAL, 255.)) ++ IVAL = MAX(0.,MIN(RVAL, 255.)) + + IF (FLIP) THEN + IVAL = 255 - IVAL +--- spider/src/hisd.f.orig 2015-05-20 21:30:04.788208000 +0200 ++++ spider/src/hisd.f 2015-05-20 21:30:29.848221000 +0200 +@@ -146,9 +146,7 @@ + & 'OUTPUT DOC FILE (OR * IF NONE)',ISOLD,APPEND,MESSAGE, + & NEWFILE,IRTFLG) + +- WANTDOC = (IRTFLG == 0) +- +- IF (WANTDOC) THEN ++ IF (IRTFLG == 0) THEN + C OUTPUT TO DOC FILE + + C 123456789 123456789 123456789 123456789 123456789 +--- spider/src/star2doc.f.orig 2015-05-20 21:41:24.588241000 +0200 ++++ spider/src/star2doc.f 2015-05-20 21:41:50.069338858 +0200 +@@ -82,6 +82,7 @@ + CHARACTER(LEN=1) :: CDUM + INTEGER :: LUNDOCT,ILOC,IT,NLIST,ILAST + INTEGER :: IHI,I,IKEY,IRTFLG,LENREC,IVAR,ITOK ++ INTEGER :: NSPI + + LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM + LOGICAL :: ADDEXT,GETNAME +--- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +@@ -14,4 +14,4 @@ + .f.a: + $(COMP) $(FFLAGS) $< + $(AR) $(AFLAGS) $(LIB) $*.o +- @\rm $*.o ++# @\rm $*.o -- GitLab From b1b0d1ed44844db6e5e773b53ea20a18b485f6f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:06:21 +0200 Subject: [PATCH 0206/1172] fix path in SPIDER patch --- .../easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 9857ea9f14..3f36cf0b41 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -61,8 +61,8 @@ LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM LOGICAL :: ADDEXT,GETNAME ---- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 -+++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +--- spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 @@ -14,4 +14,4 @@ .f.a: $(COMP) $(FFLAGS) $< -- GitLab From a54658145a7cfe4633c9958ede6b2d7e44defd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:40:43 +0200 Subject: [PATCH 0207/1172] add -mt and -mpi variants of SPIDER, extend patch --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 4 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 27 +++++++++++++ 4 files changed, 108 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb new file mode 100644 index 0000000000..051f460b6a --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mpi' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'usempi': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb new file mode 100644 index 0000000000..3638191610 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mt' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'openmp': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb index f9744a6899..cf9bac0479 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -27,9 +27,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 3f36cf0b41..57bb1f1a3d 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -69,3 +69,30 @@ $(AR) $(AFLAGS) $(LIB) $*.o - @\rm $*.o +# @\rm $*.o +--- spider/src/four_fq.f.orig 2015-05-21 10:37:01.109541000 +0200 ++++ spider/src/four_fq.f 2015-05-21 10:36:37.703908871 +0200 +@@ -1028,13 +1028,11 @@ + C BUTTERWORTH ELLIPTIC LOWPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + ELSEIF (IOPT == 12) THEN + C BUTTERWORTH ELLIPTIC HIGHPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + + ELSEIF (IOPT == 13) THEN +--- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 ++++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +@@ -1252,7 +1252,7 @@ + INCLUDE 'CMBLOCK.INC' + + INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG +- LOGICAL :: SAYIT ++ LOGICAL :: SAYIT, ENDFILE + + REAL, POINTER :: IPQ(:) + CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START -- GitLab From 9880d63fb8810ac68b62411fcfd610b43b6e7830 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:49:17 +0200 Subject: [PATCH 0208/1172] rename to R-bundle, depend on -extra bundle --- ...undle-20150520-intel-2015a-R-3.1.3-devtools.eb} | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/r/{R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb => R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb} (77%) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb similarity index 77% rename from easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index 8cb259acf8..d4a983401d 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -1,10 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundles' +name = 'R-bundle' version = '20150520' -bundlename = 'devtools' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) +versionsuffix = '-R-%s-devtools' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,30 +16,25 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.40.0'), - ('libxml2', '2.9.2'), + ('R-bundle', '20150323-R-%s-extra' % rver), ] -name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s_%(version)s.tar.gz' } # !! order of packages is important !! exts_list = [ - ('XML', '3.98-1.1', ext_options), ('memoise', '0.2.1', ext_options), ('whisker', '0.3-2', ext_options), ('rstudioapi', '0.3.1', ext_options), ('roxygen2', '4.1.1', ext_options), ('git2r', '0.10.1', ext_options), - ('RCurl', '1.95-4.6', ext_options), - ('httr', '0.6.1', ext_options), ('rversions', '1.0.0', ext_options), ('devtools', '1.8.0', ext_options), ] -- GitLab From ed31db7d4b72bef55e57e552e3daa64ead13efac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 12:20:31 +0200 Subject: [PATCH 0209/1172] rename to R-bundle, move vegan/widgetTools extensions to R easyconfig --- ...dle-20150323-intel-2015a-R-3.1.3-extra.eb} | 10 ++-- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 ------------------- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 + 3 files changed, 5 insertions(+), 54 deletions(-) rename easybuild/easyconfigs/r/{R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb => R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb} (91%) delete mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb similarity index 91% rename from easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6cd16e2bf9..108db2e37d 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-extra' +name = 'R-bundle' version = '20150323' rver = '3.1.3' -versionsuffix = '-R-%s' % rver +versionsuffix = '-R-%s-extra' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -16,8 +16,6 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('Tcl', '8.6.4'), - ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] @@ -43,11 +41,9 @@ bioconductor_options = { # !! order of packages is important !! exts_list = [ - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk - ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ('RCurl', '1.95-4.5', ext_options), # requires cURL ('XML', '3.98-1.1', ext_options), # requires libxml2 - # extensions below requires one or more extensions that have an external dependency listed above + # extensions below require one or more extensions that have an external dependency listed above ('picante', '1.6-2', ext_options), ('spacodiR', '0.13.0115', ext_options), ('picante', '1.6-2', ext_options), diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb deleted file mode 100644 index e71e3abf1d..0000000000 --- a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-extra' -rver = '3.1.2' -version = '%s-1.0.0' % rver - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [ - ('R', rver), - ('GMP', '6.0.0a'), # for gmp -] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -exts_list = [ - ('gmp', '0.5-12', ext_options), -] - -modextrapaths = {'R_LIBS': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index fefd97519c..b39267177d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From e6b4b18c41bf0c69fc9c28be5d0df1c98807a8aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 13:06:12 +0200 Subject: [PATCH 0210/1172] fix remark --- easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb index 7c9526c34b..4e2d371a71 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -16,10 +16,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -# dependencies = [('OpenSSL', '1.0.1m')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# dependencies = [('OpenSSL', '1.0.1m')] # configopts = "--with-ssl=$EBROOTOPENSSL" sanity_check_paths = { -- GitLab From f3ffb1ab5ae2797d56b71885ff0dc5992d6bcb27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:01:00 +0200 Subject: [PATCH 0211/1172] {*}[foss/2015.05] Python 2.7.9 + Boost 1.58.0 + deps --- .../Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 26 ++++ .../b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 16 +++ .../libreadline-6.3-foss-2015.05.eb | 28 +++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 16 +++ .../p/Python/Python-2.7.9-foss-2015.05.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 39 ++++++ .../t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 26 ++++ .../z/zlib/zlib-1.2.8-foss-2015.05.eb | 23 ++++ 8 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb new file mode 100644 index 0000000000..99e816f731 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb new file mode 100644 index 0000000000..94eb15f42f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 +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': 'foss', 'version': '2015.05'} +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-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000..09db15bea5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,28 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..46d3cd55d8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb new file mode 100644 index 0000000000..2e2b6decfa --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -0,0 +1,116 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 +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': 'foss', 'version': '2015.05'} +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'), +# ('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': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://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': ['http://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': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('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': ['http://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-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb new file mode 100644 index 0000000000..a84b2916e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -0,0 +1,39 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 +## +# 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': 'foss', 'version': '2015.05'} + +# 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/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb new file mode 100644 index 0000000000..c4895ce18b --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 +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': 'foss', 'version': '2015.05'} + +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/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb new file mode 100644 index 0000000000..6cb32ff060 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -0,0 +1,23 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 5981713451bb61aea69314dfd0e2dd5c45ddea0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:31:09 +0200 Subject: [PATCH 0212/1172] SPIDER: update patch, use _mp Makefile for -mp/-mpi variants --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 2 +- .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 2 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 116 +++++++++++++++++- 3 files changed, 112 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 051f460b6a..1a775fa535 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb index 3638191610..a747562bcb 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 57bb1f1a3d..957ed589cf 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -1,5 +1,7 @@ +fix syntax issues that trip Intel Fortran compiler (ifort) +author: Kenneth Hoste (HPC-UGent) --- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 -+++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 ++++ spider/src/copyfromtif.f 2015-05-21 12:04:17.049891641 +0200 @@ -88,7 +88,7 @@ INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) @@ -18,15 +20,18 @@ IF (IRTFLG .NE. 0) THEN CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) -@@ -432,7 +432,7 @@ +@@ -432,9 +432,9 @@ GOTRESU = .TRUE. ELSEIF (ITAG == 306) THEN - CDATE = CVAL(1)(1:22) + CDATE = CVAL(1:22) c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', - c & CVAL(1)(1:ICOUNT) +-c & CVAL(1)(1:ICOUNT) ++c & CVAL(1:ICOUNT) GOTDATE = .TRUE. + + ELSE --- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 +++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 @@ -269,7 +269,7 @@ @@ -85,14 +90,113 @@ ELSEIF (IOPT == 13) THEN ---- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 -+++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +--- spider/src/spider.f.orig 2015-04-21 15:30:40.000000000 +0200 ++++ spider/src/spider.f 2015-05-21 15:03:36.159704166 +0200 +@@ -195,9 +195,15 @@ + + #ifndef USE_MPI + #ifndef __APPLE__ ++#ifdef SP_IFC ++ isiz1 = kmp_get_stacksize() ++ CALL kmp_set_stacksize(65536) ++ isiz2 = kmp_get_stacksize() ++#else + isiz1 = omp_get_stack_size() + CALL omp_set_stack_size(65536) + isiz2 = omp_get_stack_size() ++#endif + !write(6,*) ' OMP Stack size: ',isiz1,' -->',isiz2 + + #endif +--- spider/src/lundoc.f.orig 2015-03-27 14:08:10.000000000 +0100 ++++ spider/src/lundoc.f 2015-05-21 15:26:30.008871936 +0200 @@ -1252,7 +1252,7 @@ INCLUDE 'CMBLOCK.INC' INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG - LOGICAL :: SAYIT -+ LOGICAL :: SAYIT, ENDFILE ++ LOGICAL :: SAYIT, EOF REAL, POINTER :: IPQ(:) CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START +@@ -1319,15 +1319,15 @@ + BACKSPACE(NDOC) ! REREAD LINE + READ(NDOC,*,END=100,IOSTAT=IER) RECLIN + +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ(NDOC,*,END=100,IOSTAT=IER) NKEY,NREGPLINE +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + +- 100 CALL BCAST_MPI('LUNDOCINFO','ENDFILE',ENDFILE,1,'L',ICOMM) ++ 100 CALL BCAST_MPI('LUNDOCINFO','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','IER',IER,1,'I',ICOMM) +- IF (ENDFILE) GOTO 799 ++ IF (EOF) GOTO 799 + + CALL BCAST_MPI('LUNDOCINFO','NKEY',NKEY,1,'I',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','NREGPLINE',NREGPLINE,1, +@@ -1434,7 +1434,7 @@ + + REAL :: PLIST(*) + CHARACTER(LEN=180) :: RECLIN +- LOGICAL :: TILLEND ++ LOGICAL :: TILLEND, EOF, ERRFILE + + CALL SET_MPI(ICOMM,MYPID,MPIERR) ! SETS ICOMM AND MYPID + +@@ -1464,18 +1464,18 @@ + 10 CONTINUE + IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=200) RECLIN + 81 FORMAT(A120) + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + 100 CALL BCAST_MPI('LUNDOCGETCOM','ERRFILE',ERRFILE,1,'L',ICOMM) + IF (ERRFILE) GOTO 998 + +-200 CALL BCAST_MPI('LUNDOCGETCOM','ENDFILE',ENDFILE,1,'L',ICOMM) +- IF (ENDFILE) GOTO 997 ++200 CALL BCAST_MPI('LUNDOCGETCOM','EOF',EOF,1,'L',ICOMM) ++ IF (EOF) GOTO 997 + + CALL BCAST_MPI('LUNDOCGETCOM','RECLIN',RECLIN,180,'C',ICOMM) + +@@ -1580,7 +1580,7 @@ + CHARACTER *120 RECLIN + #ifdef USE_MPI + include 'mpif.h' +- LOGICAL ENDFILE, ERRFILE ++ LOGICAL EOF, ERRFILE + ICOMM = MPI_COMM_WORLD + CALL MPI_COMM_RANK(ICOMM, MYPID, MPIERR) + #else +@@ -1595,15 +1595,15 @@ + #ifdef USE_MPI + 10 IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=100) RECLIN + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + +-100 CALL BCAST_MPI('LUNDOCSAYHDR','ENDFILE',ENDFILE,1,'L',ICOMM) ++100 CALL BCAST_MPI('LUNDOCSAYHDR','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCSAYHDR','ERRFILE',ERRFILE,1,'L',ICOMM) +- IF (ENDFILE .OR. ERRFILE) GOTO 999 ++ IF (EOF .OR. ERRFILE) GOTO 999 + + CALL BCAST_MPI('LUNDOCSAYHDR','RECLIN',RECLIN,120,'C',ICOMM) + #else -- GitLab From 7962d2cba1c7cd60964509de65f0b96a257106ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:35:47 +0200 Subject: [PATCH 0213/1172] add patch for installing paycheck as Py3 extension --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ ...aycheck-1.0.2_setup-open-README-utf8.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c5e5b4ddcb..d79f2b54ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -55,6 +55,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], diff --git a/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..193336def4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,22 @@ +open README file with utf-8 encoding, to avoid error like: +UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 577: ordinal not in range(128) +author: Kenneth Hoste (HPC-UGent) +--- paycheck-1.0.2/setup.py.orig 2015-05-21 16:09:24.300074046 +0200 ++++ paycheck-1.0.2/setup.py 2015-05-21 16:11:43.503945542 +0200 +@@ -1,6 +1,7 @@ + from distutils.cmd import Command + from distutils.core import setup + ++import codecs + import sys + if sys.version_info >= (3, 0): + try: +@@ -24,7 +25,7 @@ + name = 'paycheck', + version ='1.0.2', + description ='A Python QuickCheck implementation', +- long_description = open("README.txt").read(), ++ long_description = codecs.open("README.txt", encoding='utf-8').read(), + author ='Mark Chadwick', + author_email ='mark.chadwick@gmail.com', + maintainer ='Gregory Crosswhite', -- GitLab From 2294aff5b5e3a456e7598f75d227a55b0454b5c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:38:30 +0200 Subject: [PATCH 0214/1172] fix remark --- .../b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 1 - easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb | 1 - 8 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb index 99e816f731..24316a807f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 name = 'Boost' version = '1.58.0' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb index 94eb15f42f..1c3c8d1851 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 name = 'bzip2' version = '1.0.6' 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 09db15bea5..c23d9ba711 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 @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 easyblock = 'ConfigureMake' name = 'libreadline' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 46d3cd55d8..63b54fa7c4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 2e2b6decfa..ce15e506fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 name = 'Python' version = '2.7.9' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb index a84b2916e1..5e77859d07 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb index c4895ce18b..bd202e0e1b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 easyblock = 'ConfigureMake' name = 'Tcl' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb index 6cb32ff060..7668682872 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 easyblock = 'ConfigureMake' name = 'zlib' -- GitLab From 9884eda25ed3c0acd92494e121676cf6519bffae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 17:14:31 +0200 Subject: [PATCH 0215/1172] fix mpi variant of SPIDER --- .../easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 1a775fa535..cdcacc4631 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -9,7 +9,7 @@ description = """SPIDER (System for Processing Image Data from Electron microsco an image processing system for electron microscopy.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'static': True, 'usempi': True} +toolchainopts = {'usempi': True} source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] sources = ['spiderweb.%(version)s.tar.gz'] @@ -28,7 +28,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS -ldl -lpthread"' modextrapaths = {'PATH': ['spider/bin']} -- GitLab From e3f796267c030c4988e24274c0074483a8681d04 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 May 2015 18:23:16 +0200 Subject: [PATCH 0216/1172] CHARMM for intel/2015a --- .../c/CHARMM/CHARMM-37b2-intel-2015a.eb | 28 ++++++++++ ...CHARMM-37b2_fix-qgas-double-declared.patch | 53 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb new file mode 100644 index 0000000000..155eb5a8ae --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = "CHARMM" +version = "37b2" + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch new file mode 100644 index 0000000000..2c8d36a45f --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch @@ -0,0 +1,53 @@ +reproduction of CHARMM SVN revision 272 (Check-in: http:/charmm.hanyang.ac.kr/6187) +renamed qgas variable in pbeq to qgas1 and updated references in energy +diff -ru c37b2.orig/source/energy/energy.src c37b2/source/energy/energy.src +--- c37b2.orig/source/energy/energy.src 2012-09-29 08:01:42.000000000 +0200 ++++ c37b2/source/energy/energy.src 2015-05-21 16:57:43.951197202 +0200 +@@ -266,7 +266,7 @@ + use param + use pathm + use mpathint, only: qpint, epint !##PATHINT +- use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas,qsmbp,smbp0 !##PBEQ ++ use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas1,qsmbp,smbp0 !##PBEQ + use pbound + use pert + use polarm, only: qpolar, polar1 !##POLAR +@@ -3203,7 +3203,7 @@ + + CALL PBFORCE(NATOM,X,Y,Z,CG,ETERM(PBELEC),ETERM(PBNP), & + DX,DY,DZ,NPBEQ,ecalls,.false. & +- ,QETERM(QMEL),ETERM(QMEL),QGAS & !##SCCDFTB ++ ,QETERM(QMEL),ETERM(QMEL),QGAS1 & !##SCCDFTB + ) + IF (TIMER.GT.1) & + CALL WRTTIM('Poisson Boltzmann Solvation energy times:') +diff -ru c37b2.orig/source/misc/pbeq.src c37b2/source/misc/pbeq.src +--- c37b2.orig/source/misc/pbeq.src 2012-08-08 20:08:30.000000000 +0200 ++++ c37b2/source/misc/pbeq.src 2015-05-21 16:55:47.871787533 +0200 +@@ -19,7 +19,7 @@ + !public :: pbeq0,pbforce,gsbp0,srdist + !QC: export more + public :: pbeq0,pbforce,gsbp0,srdist,m3,dm3,rpowerl2,cosmphi2,sinmphi2,& +- alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas, & ++ alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas1, & + pbeq_iniall,smbp0 + + !variables +@@ -115,7 +115,7 @@ + + ! The following is related to QM/MM implementation of gsbp and pb + ! Xiao_QC_UW0609 +- LOGICAL QPSC,QGAS ++ LOGICAL QPSC,QGAS1 + ##IF SCCDFTB + ! + ! COEFX -----> heap index for COEFX(NTPOL) +@@ -2734,7 +2734,7 @@ + ! XIAO_QC_UW0609 keyword for SCC/PB + MXTPSC = GTRMI(COMLYN,COMLEN,'MXPS',5000) + PSCTOL = GTRMF(COMLYN,COMLEN,'PSTL',1.0D-2) +- QGAS = INDXA(COMLYN,COMLEN,'IGAS').GT.0 ++ QGAS1 = INDXA(COMLYN,COMLEN,'IGAS').GT.0 + ! XIAO_QC_UW0609 add charge dependant radii + QCHDRAD = INDXA(COMLYN,COMLEN,'CHDR').GT.0 + IF (QCHDRAD) THEN -- GitLab From 2642b0323b03578be61758ff225fb8effb98dac6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:09:11 +0200 Subject: [PATCH 0217/1172] add patch for installing deap as Py3 extension --- .../p/Python/Python-3.4.1-intel-2014b.eb | 6 ++++++ .../p/Python/Python-3.4.1-intel-2015a.eb | 6 ++++++ .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ .../deap-1.0.2_setup-open-README-utf8.patch | 17 +++++++++++++++++ 4 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 07f5694321..49334fee76 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index ba75d726f9..8ddd32db67 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d79f2b54ad..a71f6ecf62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -81,6 +81,9 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..6dece6f5d8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.2.orig/setup.py 2015-05-12 04:06:49.000000000 +0200 ++++ deap-1.0.2/setup.py 2015-05-21 19:06:03.792820042 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -10,7 +11,7 @@ + from pypandoc import convert + except ImportError: + print("warning: pypandoc module not found, could not convert Markdown to RST") +- read_md = lambda f: open(f, 'r').read() ++ read_md = lambda f: codecs.open(f, encoding='utf-8').read() + else: + read_md = lambda f: convert(f, 'rst') + -- GitLab From 4e5c4223b6c9fe5010909f037306404fef1a24ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:25:22 +0200 Subject: [PATCH 0218/1172] bump rtracklayer version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 108db2e37d..42f13415a0 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -51,7 +51,7 @@ exts_list = [ ('tkWidgets', '1.44.0', bioconductor_options), ('Mfuzz', '2.26.0', bioconductor_options), ('maSigPro', '1.38.0', bioconductor_options), - ('rtracklayer', '1.26.2', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), ('BSgenome', '1.34.1', bioconductor_options), ('GEOquery', '2.32.0', bioconductor_options), ('biomaRt', '2.22.0', bioconductor_options), -- GitLab From 929ead97b4a3abcee028477e385cb3c4fe6ab2e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:34:47 +0200 Subject: [PATCH 0219/1172] bump GenomicFeatures version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 42f13415a0..6fa810b17b 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -62,7 +62,7 @@ exts_list = [ ('GOstats', '2.32.0', bioconductor_options), ('geneplotter', '1.44.0', bioconductor_options), ('DESeq2', '1.6.3', bioconductor_options), - ('GenomicFeatures', '1.18.4', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), ('VariantAnnotation', '1.12.9', bioconductor_options), ('biovizBase', '1.14.1', bioconductor_options), ('OrganismDbi', '1.8.1', bioconductor_options), -- GitLab From 50b099be684215bc154f134486e6a16d856bed98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:47:36 +0200 Subject: [PATCH 0220/1172] bump KEGGprofile version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6fa810b17b..732d498ea8 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -78,7 +78,7 @@ exts_list = [ ('Homo.sapiens', '1.1.2', bioconductor_options), ('KEGGgraph', '1.24.0', bioconductor_options), ('KEGGREST', '1.6.4', bioconductor_options), - ('KEGGprofile', '1.8.0', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), -- GitLab From bed4ccdb0fe734f652941f2bf890ae4792000c92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:59:16 +0200 Subject: [PATCH 0221/1172] bump GViz version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 732d498ea8..a6d53af385 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -82,7 +82,7 @@ exts_list = [ ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), - ('Gviz', '1.10.10', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), ('methyAnalysis', '1.8.0', bioconductor_options), ('pathview', '1.6.0', bioconductor_options), ('SPIA', '2.18.0', bioconductor_options), -- GitLab From 1c264c26a5d5c529eb5cc583f7fb2a4458a7b0dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 21:09:56 +0200 Subject: [PATCH 0222/1172] move vegan/widgetTools extensions to R foss/2015a easyconfig --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 5d7d661a1f..26e352af95 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From 9cdee34afd8e5216d72b171cb7b50f3879f4e3fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 22:29:45 +0200 Subject: [PATCH 0223/1172] include deap v1.0.1 specific patch --- .../p/Python/Python-3.4.1-intel-2014b.eb | 2 +- .../p/Python/Python-3.4.1-intel-2015a.eb | 2 +- .../deap-1.0.1_setup-open-README-utf8.patch | 17 +++++++++++++++++ 3 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 49334fee76..d3f83f3c59 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 8ddd32db67..9f71e6e86f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch new file mode 100644 index 0000000000..b7c896999f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.1.orig/setup.py 2014-04-08 15:49:52.000000000 +0200 ++++ deap-1.0.1/setup.py 2015-05-21 22:25:37.345008000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -11,7 +12,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=open('README.txt').read(), ++ long_description=codecs.open('README.txt', encoding='utf-8').read(), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='http://deap.googlecode.com', -- GitLab From 52bf9f7fd6f8803d4ee3f59c3b27f6c5a5ffc0f7 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 21 May 2015 22:35:33 -0400 Subject: [PATCH 0224/1172] fixed git to include EB perl and path --- .../easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 3 +- .../easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb | 46 +++++++++++++++++++ 2 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb 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 48bda49ebe..ceec29fe23 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 @@ -29,12 +29,13 @@ 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 = "--enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..d03af57112 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.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 +# Authors:: Dmitri Gribenko +# 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 = 'git' +version = '2.4.1' + +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': 'GCC', 'version': '4.9.2'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +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'" + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 54ddbfbfdc33fa68c1ff125bca4e3783e3088d4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 May 2015 10:18:44 +0200 Subject: [PATCH 0225/1172] fix versionsuffix for extra R-bundle dep --- .../R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index d4a983401d..5a2b464944 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -16,7 +16,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('R-bundle', '20150323-R-%s-extra' % rver), + ('R-bundle', '20150323', '-R-%s-extra' % rver), ] ext_options = { -- GitLab From d3d92f131d3efdaabfe60b03eb261de2f1730ebf Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 11:24:24 +0200 Subject: [PATCH 0226/1172] OpenFOAM foss 2015.05 flavour: needed for Centos6 on Haswell --- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb new file mode 100644 index 0000000000..14bd0cffc2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -0,0 +1,58 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +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': 'foss', 'version': '2015.05'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432217883, + "build_time": 2389.2, + "install_size": 1888270856, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From 757910d0c00fcd3f85f4367e5fb29e55b92f4081 Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 12:15:43 +0200 Subject: [PATCH 0227/1172] adding missing libreadline,SCOTCH,ncurses,flex --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 40 ++++++++++++++ .../libreadline-6.3-foss-2015.05.eb | 53 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 48 +++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 40 ++++++++++++++ 4 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb new file mode 100644 index 0000000000..4e10bab03a --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215494, + "build_time": 21.24, + "install_size": 2865429, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] 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 new file mode 100644 index 0000000000..1ad6cea720 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,53 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215473, + "build_time": 17.27, + "install_size": 2395805, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..5ba0974ce8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,48 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215455, + "build_time": 80.56, + "install_size": 24625439, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb new file mode 100644 index 0000000000..e388e08516 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 +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': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215375, + "build_time": 70.85, + "install_size": 6501533, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From a70c7d4b41166f23af8d4a68311170c86dd1594f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 14:28:00 +0200 Subject: [PATCH 0228/1172] cleaned comments in flex-2.5.39-foss-2015.05.eb libreadline-6.3-foss-2015.05.eb ncurses-5.9-foss-2015.05.eb OpenFOAM-2.3.1-foss-2015.05.eb SCOTCH-6.0.4-foss-2015.05.eb --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 25 ------------------- .../libreadline-6.3-foss-2015.05.eb | 25 ------------------- .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 25 ------------------- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 25 ------------------- .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 25 ------------------- 5 files changed, 125 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 4e10bab03a..5f048f3577 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 name = 'flex' version = '2.5.39' @@ -14,27 +13,3 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215494, - "build_time": 21.24, - "install_size": 2865429, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] 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 1ad6cea720..93acd649a7 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 @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 easyblock = 'ConfigureMake' name = 'libreadline' @@ -27,27 +26,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215473, - "build_time": 17.27, - "install_size": 2395805, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 5ba0974ce8..e8393ca7cf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 name = 'ncurses' version = '5.9' @@ -22,27 +21,3 @@ configopts = [ moduleclass = 'devel' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215455, - "build_time": 80.56, - "install_size": 24625439, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 14bd0cffc2..6f0594b990 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 name = 'OpenFOAM' version = '2.3.1' @@ -32,27 +31,3 @@ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432217883, - "build_time": 2389.2, - "install_size": 1888270856, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index e388e08516..25db821e80 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 name = 'SCOTCH' version = '6.0.4' @@ -14,27 +13,3 @@ sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215375, - "build_time": 70.85, - "install_size": 6501533, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From ec29cc694ff50160a089ce904e308b967912d93f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 15:11:53 +0200 Subject: [PATCH 0229/1172] a byte cleaner ;) --- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 5f048f3577..208a02e540 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -12,4 +12,3 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' - 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 93acd649a7..c23d9ba711 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 @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index e8393ca7cf..3ab27d3a62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -20,4 +20,3 @@ configopts = [ ] moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 6f0594b990..9e1b2ca02b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -30,4 +30,3 @@ dependencies = [ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' - diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index 25db821e80..f5bdd9828b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -12,4 +12,3 @@ source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' - -- GitLab From ae63f1c4b91fbb4ed2ba8a4966887b4f4185c404 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 09:41:18 +0200 Subject: [PATCH 0230/1172] Update to Clang 3.6.1 --- .../c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..15c22eef9c --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.1" + +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': '4.9.2'} +# 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", +] + +dependencies = [ + ('GMP', '6.0.0'), + ('ISL', '0.14'), +] + +builddependencies = [ + ('CMake', '3.2.1'), + ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' -- GitLab From 84c98379f747142ef37eaa45900c867af0f792cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:04:16 +0200 Subject: [PATCH 0231/1172] fix GMP 6.0.0a with GCC/4.9.2 --- .../c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- 4 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 445ace0985..40f0a86d6f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index 08df157950..df7b8848c5 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -9,7 +9,7 @@ operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = ["%(namelower)s-%(version)sa.tar.bz2"] +sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb new file mode 100644 index 0000000000..a9855e2029 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.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': 'GCC', 'version': '4.9.2'} + +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 3ba25676db..f6423e5d6e 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -dependencies = [('GMP', '6.0.0')] +dependencies = [('GMP', '6.0.0a')] sanity_check_paths = { 'files': ['lib/libisl.so', 'lib/libisl.a'], -- GitLab From 6f3f4dcf481be0bd3542527498c81f8346bf0a11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:30:48 +0200 Subject: [PATCH 0232/1172] {bio}[dummy] fastqc 0.11.2 + 0.11.3 --- .../easyconfigs/f/fastqc/fastqc-0.11.2.eb | 27 +++++++++++++++++++ .../easyconfigs/f/fastqc/fastqc-0.11.3.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb new file mode 100644 index 0000000000..9ff730ebed --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_60')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb new file mode 100644 index 0000000000..c5f20b9165 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.3' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 0af5491f63d43f506f1382e7c4b8b03394f31089 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 11:59:09 +0200 Subject: [PATCH 0233/1172] Change name of gmp version --- easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb index 15c22eef9c..966759d71c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] -- GitLab From ac56b0de721ee0821608eb2d6a84be210e2c4ac1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 14:42:17 +0200 Subject: [PATCH 0234/1172] add fpp + deps as R extensions --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 4 ++++ easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 26e352af95..dee61f1e01 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index b39267177d..d50dfde38a 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From e1c84d962128346b1073db16e6f069a8d4acbec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 11:13:08 +0200 Subject: [PATCH 0235/1172] include patch to build forecast with Intel compilers --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index d50dfde38a..56604be04c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,7 +382,7 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), diff --git a/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch new file mode 100644 index 0000000000..8582ea93ae --- /dev/null +++ b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch @@ -0,0 +1,9 @@ +ignore warning/error when building with Intel C++ compiler by including -wd308 flag in $CXXFLAGS +author: Kenneth Hoste (HPC-UGent) +--- forecast/src/Makevars.orig 2015-05-12 11:56:10.000000000 +0200 ++++ forecast/src/Makevars 2015-05-28 10:53:13.878100139 +0200 +@@ -1,2 +1,4 @@ + ## Use the R_HOME indirection to support installations of multiple R version + PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From ac6d71a57e7784a9017eb7d5416c05efb0088eca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:47:03 +0200 Subject: [PATCH 0236/1172] {lang}[intel/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-intel-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb new file mode 100644 index 0000000000..e42c4eb9ce --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +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': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb new file mode 100644 index 0000000000..7f1dc7e31f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015a'} + +# 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', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9a43d2783570dc62fe774b79cd59b0143b8c8e04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:49:18 +0200 Subject: [PATCH 0237/1172] {lang}[foss/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-foss-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb new file mode 100644 index 0000000000..16e9072248 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb new file mode 100644 index 0000000000..d5bf2693bd --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# 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', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a39319427c8e4fd76769bf875504e4403f245705 Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Thu, 28 May 2015 12:53:15 +0200 Subject: [PATCH 0238/1172] NEMO easyconfig --- .../easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb new file mode 100644 index 0000000000..cc73946e3e --- /dev/null +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb @@ -0,0 +1,15 @@ +name = 'NEMO' +version = '3.4' + +homepage = 'http://www.nemo-ocean.eu/' +description = 'NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies.' + +toolchain = {'name': 'ictce','version': '6.1.5'} +toolchainopts = {'opt': False, 'optarch': False} + +with_components = ['OPA_SRC', 'LIM_SRC_3'] +add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] +del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] -- GitLab From bcdea025bfc604af17e7d4e6b7d2b60796af2937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:33:19 +0200 Subject: [PATCH 0239/1172] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 7f1dc7e31f..03c9b50fba 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 8ab6b2e829ee34003022ad74349f38f9ffb9ce50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:34:51 +0200 Subject: [PATCH 0240/1172] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index d5bf2693bd..fbe46bacc9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 7d572304650bd03f278d32035f5665c3a7577f22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:36:46 +0200 Subject: [PATCH 0241/1172] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 16e9072248..08ae2a5f52 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 8ec777916625061646218da5cccda84090b7e1ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:37:01 +0200 Subject: [PATCH 0242/1172] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index e42c4eb9ce..5691adf05e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 3882c4aaaed7c4227813b84110b97205f92eb9e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:07:40 +0200 Subject: [PATCH 0243/1172] {phys}[intel/2015a] Geant4 10.01.p01 --- .../c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 19 +++++++++++++++ .../g/Geant4/Geant4-10.01.p01-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb new file mode 100644 index 0000000000..c165bda92e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.5' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb new file mode 100644 index 0000000000..412c19225c --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '10.01.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.2.0.5'), +] + +builddependencies = [('CMake', '3.2.2')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' -- GitLab From 9ec1a46de2390d2d455c64ffc2f10606f4d73db5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:45:52 +0200 Subject: [PATCH 0244/1172] add missing CMake build dep --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb index c165bda92e..9408c50361 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +builddependencies = [('CMake', '3.2.2')] + separate_build_dir = True moduleclass = 'numlib' -- GitLab From 84c0c0920951a011d2b4514910b746da00c5ebc2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 10:55:58 +0200 Subject: [PATCH 0245/1172] added gcc 4.5.2 --- easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb | 37 ++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb new file mode 100644 index 0000000000..719bc6f315 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.5.2' + +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': 'dummy'} + +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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.2.tar.gz', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.8.2.tar.gz', +] + +checksums = [ + 'e31fe695d7235f11fb5a63eafdfbfe88', # gcc-4.5.2.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' -- GitLab From 43055375813abdc4dff967afd008353b5646839e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 11:03:50 +0200 Subject: [PATCH 0246/1172] Added GCC 4.6.0 --- easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb | 35 ++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb new file mode 100644 index 0000000000..f310421ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.6.0' + +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': 'dummy'} + +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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.9.tar.gz', +] + +checksums = [ + '009f59ee0f9c8100c12939140698cf33', # gcc-4.6.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + +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 a396d464cc65eba9b7d35613d13be752d63a1e43 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 29 May 2015 11:48:02 +0200 Subject: [PATCH 0247/1172] Add hanythingondemand eb files. These could otherwise have been installed w/ --try-software-version --- ...ondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6063d9ec3 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.2' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..9182229d2c --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.3' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..73433b3081 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.4' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' -- GitLab From 87a8597e5c07722acbe0a06dd001bcf9b04e368d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 May 2015 14:07:44 +0200 Subject: [PATCH 0248/1172] style fixes in pBWA easyconfig --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index 754be559e1..fa5b729bcb 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -13,7 +13,7 @@ name = 'pBWA' version = '0.5.9_1.21009' homepage = 'http://pbwa.sourceforge.net/' -description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" +description = "pBWA is a parallel implementation of the popular software BWA." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} @@ -21,18 +21,13 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(name)s_%(version)s.zip'] source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] - - -dependencies = [ - ('BWA', '0.7.4'), -] +dependencies = [('BWA', '0.7.4')] files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] sanity_check_paths = { - 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], - 'dirs': ['.'], - + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], } moduleclass = 'bio' -- GitLab From 3b0eec5db69770911d52947e78b1f89df48c5824 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:00:43 +0200 Subject: [PATCH 0249/1172] Adding ABySS-1.5.2-goolf-1.4.10 --- .../a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..678a7abd6f --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.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 +# 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_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.5.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] + +dependencies = [('Boost', '1.53.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c5a863a5e45f620767357721fc87bc880f47759b Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:14:18 +0200 Subject: [PATCH 0250/1172] Adding BEDTools-2.23.0-goolf-1.4.10 --- .../BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6dd7cdc664 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +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': 'goolf', 'version': '1.4.10'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] +sources = ['v%(version)s/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 df353b92cb8dc3d0023eb54ee401cc53622365a5 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:21:00 +0200 Subject: [PATCH 0251/1172] Comments modifications --- easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb index 678a7abd6f..c055778c8e 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -2,12 +2,10 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos +# Authors:: Maxime Schmitt , 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' @@ -21,9 +19,8 @@ description = """Assembly By Short Sequences - a de novo, parallel, paired-end s toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} -# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [('Boost', '1.53.0')] -- GitLab From 440afe75a71962fb1c166bc2918f0735000d14de Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:23:50 +0200 Subject: [PATCH 0252/1172] Modifying comments --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 6dd7cdc664..61147b9331 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -1,4 +1,6 @@ -# Author: Pablo Escobar Lopez +# Author: Maxime Schmitt, University of Luxembourg +# +# Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel -- GitLab From ec543429de043b66a96a3c9df79887ea6bcd0886 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:34:14 +0200 Subject: [PATCH 0253/1172] Adding Cufflinks-2.2.1-goolf-1.4.10 --- .../Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb 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 new file mode 100644 index 0000000000..9897454369 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['cufflinks-2.2.1.tar.gz'] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c2c18d4e50385d295f2bddd919b09410c0a7887a Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:35:34 +0200 Subject: [PATCH 0254/1172] Fixing hardcoded version --- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 9897454369..3fdf2a0923 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 @@ -7,7 +7,7 @@ description = """Transcript assembly, differential expression, and differential toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['cufflinks-2.2.1.tar.gz'] +sources = ['cufflinks-%(version)s.tar.gz'] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] dependencies = [ -- GitLab From d09ca49609ada079f83cd2fe185768a3fab2eb23 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:39:37 +0200 Subject: [PATCH 0255/1172] Fixing source url --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 61147b9331..0c511d17e0 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -17,8 +17,8 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'goolf', 'version': '1.4.10'} # https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz -source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] -sources = ['v%(version)s/bedtools-%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -- GitLab From ea33e462b738dabf5a7599968dbaef758b8a0b2c Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:51:37 +0200 Subject: [PATCH 0256/1172] Adding Cython-0.22-goolf-1.4.10-Python-2.7.3.eb --- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d2b4a22df9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.22' + +homepage = 'http://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) +cythonlibdir = '/'.join([pylibdir, cythonsubdir]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], +} + +moduleclass = 'lang' -- GitLab From 6915caae459b0f8b730e8b972ee3b98adaa93d9d Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:03:08 +0200 Subject: [PATCH 0257/1172] Adding R-3.2.0-ictce-7.3.5 and its dependencies --- .../libjpeg-turbo-1.4.0-ictce-7.3.5.eb | 24 +++++++++++++++ .../l/libpng/libpng-1.6.17-ictce-7.3.5.eb | 19 ++++++++++++ .../libreadline-6.3-ictce-7.3.5.eb | 29 +++++++++++++++++++ .../n/NASM/NASM-2.11.06-ictce-7.3.5.eb | 19 ++++++++++++ .../n/ncurses/ncurses-5.9-ictce-7.3.5.eb | 15 ++++++++++ .../r/R/R-3.2.0-ictce-7.3.5-bare.eb | 27 +++++++++++++++++ .../z/zlib/zlib-1.2.8-ictce-7.3.5.eb | 22 ++++++++++++++ 7 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb new file mode 100644 index 0000000000..24b1cf1a07 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb new file mode 100644 index 0000000000..c2db01ab34 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000..34ea8a516d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -0,0 +1,29 @@ +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '5.9')] + +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/NASM/NASM-2.11.06-ictce-7.3.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb new file mode 100644 index 0000000000..d2c0dab761 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +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/n/ncurses/ncurses-5.9-ictce-7.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb new file mode 100644 index 0000000000..a12e472663 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb @@ -0,0 +1,15 @@ +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb new file mode 100644 index 0000000000..cf66631597 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb new file mode 100644 index 0000000000..8254f78ac9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b2e3c06deb1e415505a3d7d1423a7fc39ca30902 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:28:06 +0200 Subject: [PATCH 0258/1172] Better use of variables --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index d2b4a22df9..55a97c1d73 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -14,11 +14,9 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -pylibdir = 'lib/python%s/site-packages' % pythonshortver -cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) -cythonlibdir = '/'.join([pylibdir, cythonsubdir]) versionsuffix = '-%s-%s' % (python, pythonver) +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From 10be91757f584afc2df8650f144182daa8338505 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:42:55 +0200 Subject: [PATCH 0259/1172] Fixing name resolutions --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 55a97c1d73..08f3c850f6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py' + pyshortver + '-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From b732ac55bea37f13023094e0bedaca2f0cb8d15c Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 18:25:10 +0200 Subject: [PATCH 0260/1172] Adding Tcl/Tk dependencies, modifying Java version and fixing version error in libpng --- .../l/libpng/libpng-1.6.17-ictce-7.3.5.eb | 2 +- .../t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 50 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb index c2db01ab34..fd641ddebc 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libpng' -version = '1.6.12' +version = '1.6.17' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb new file mode 100644 index 0000000000..ab1bbc53d3 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.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': 'ictce', 'version': '7.3.5'} + +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-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb new file mode 100644 index 0000000000..2363e89fc9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -0,0 +1,24 @@ +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': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 7739627e35c49cff90c67712ea8af592f3b73509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 13:44:11 +0200 Subject: [PATCH 0261/1172] fix typo, remove unneeded configopts --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index e5ab48448f..25c6d013bc 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -17,8 +17,7 @@ checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' -configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' -configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' dependencies = [ ('libxc', '2.2.2'), -- GitLab From 553df5b666baa5856f9ccac51602e323a27b9d78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 14:48:19 +0200 Subject: [PATCH 0262/1172] {chem}[intel/2015a] ABINIT 7.10.4 --- .../a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb new file mode 100644 index 0000000000..955b1cd4f1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' -- GitLab From c67a9ec7774a9c9f488781a504cf51ab135cf180 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:06 +0200 Subject: [PATCH 0263/1172] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 955b1cd4f1..24a268901b 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 050fa061b42d083907090abebe3df8017142b871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:23 +0200 Subject: [PATCH 0264/1172] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 25c6d013bc..51c5aef3d9 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 57168333ad91183825fc00bbb34cc0322bcbdccd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:13 +0200 Subject: [PATCH 0265/1172] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 51c5aef3d9..97bc886c26 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 0f48dfa2c9bc9443825325f101a985d9e306ae5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:35 +0200 Subject: [PATCH 0266/1172] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 24a268901b..7561f6f45c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 6857cd98a5c3de64c6a53265cd490c4da464b4a9 Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 10:37:53 +0200 Subject: [PATCH 0267/1172] Gromacs 5.0.5-intel2015a easycofig --- .../GROMACS-5.0.5-intel-2015a-hybrid.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..09ed0e7dc1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-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 = '5.0.5' +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', '3.1.0'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 73db870ee8050759cb01d991f35404ca5d37887f Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 17:35:50 +0200 Subject: [PATCH 0268/1172] Gromacs 5.0.5-intel2015a easycofig --- .../easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb index 09ed0e7dc1..c7e0273a3e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -25,10 +25,10 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.1.0'), + ('CMake', '3.2.2'), ('libxml2', '2.9.2') ] -dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] moduleclass = 'bio' -- GitLab From bd81df67d7ee4ce73bb19e2869d24077f280b9fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Jun 2015 18:59:22 +0200 Subject: [PATCH 0269/1172] fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 3 +-- 10 files changed, 10 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 9409f95fc2..89cf3c3778 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index 4a03ccc94b..ec449db284 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index d97dae5c5d..476628bcd5 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index d7fb61f42c..e0dbe69249 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 04f547b28a..0b54c5912d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index 479e526fb3..c6b5e835da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index 1b9a405ed8..a5a5338771 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 5740815aa1..9007ee9bb7 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index bf87cf39af..f4b21d4cab 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index a341ebad38..aa0ea72322 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ -- GitLab From be2f94d281c7560934c72b997676ac1b65dceac7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 09:42:46 +0200 Subject: [PATCH 0270/1172] fix remark --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 2 +- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 89cf3c3778..d000d6ec7f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index ec449db284..a34afc570a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index 476628bcd5..5ef2e6d1b1 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index e0dbe69249..1e036026da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 0b54c5912d..464f263647 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index c6b5e835da..cd0fac60cb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index a5a5338771..9533b73dfd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 9007ee9bb7..b3212736f0 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index f4b21d4cab..ae347ad0bd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index aa0ea72322..2a054ef2d3 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] 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 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] -- GitLab From f0b78c2b17b0111a3369d9987b94c32d70b0156f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:29:40 +0200 Subject: [PATCH 0271/1172] {vis}[intel/2015a] libXScrnSaver 1.2.2 + libXft 2.3.2 --- .../fontconfig-2.11.93-intel-2015a.eb | 22 ++++++++++++ .../k/kbproto/kbproto-1.0.7-intel-2015a.eb | 19 +++++++++++ .../libXScrnSaver-1.2.2-intel-2015a.eb | 24 +++++++++++++ .../libXft-2.3.2-intel-2015a-libX11-1.6.3.eb | 34 +++++++++++++++++++ .../libXrender-0.9.9-intel-2015a.eb | 28 +++++++++++++++ .../renderproto-0.11-intel-2015a.eb | 20 +++++++++++ 6 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb new file mode 100644 index 0000000000..77235f32a1 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000..62923f260f --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.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': 'intel', 'version': '2015a'} + +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/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000..0889930509 --- /dev/null +++ b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXScrnSaver' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Screen Saver extension client library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3') +] + +sanity_check_paths = { + 'files': ['lib/libXss.a', 'lib/libXss.so', 'include/X11/extensions/scrnsaver.h'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..65123b2fae --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb new file mode 100644 index 0000000000..393ccdfa93 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('renderproto', '0.11'), +] + +dependencies = [ + ('kbproto', '1.0.7'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb new file mode 100644 index 0000000000..b1d4936121 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.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': 'intel', 'version': '2015a'} +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 b559f80695feb569bbee527ed6d64fae204ced1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:48:47 +0200 Subject: [PATCH 0272/1172] include Tk as dependency in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015.05.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a.eb | 1 + .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 1 + .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a.eb | 1 + .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb | 24 ++++++++++++++++++ 16 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 3974b6e842..e9840cb7eb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index ce15e506fc..0fa5529cb0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 669c54c38d..5eed3b0154 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 3273aa0399..1ff5189a78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e206b78e22..2f9941dfab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,6 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 9a1f9af5fc..536743d8c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2c02867a9..499a28228b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 95f4d38205..71a627c500 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-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 ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..fcf9fcc830 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.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': 'GCC', 'version': '4.9.2'} + +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/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb new file mode 100644 index 0000000000..a933eab557 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.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': 'foss', 'version': '2015.05'} + +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/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb new file mode 100644 index 0000000000..099c4a95f4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.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': 'gompi', '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' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..150f56cf00 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.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': 'goolf', 'version': '1.5.14'} + +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-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb new file mode 100644 index 0000000000..3530d74282 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb @@ -0,0 +1,24 @@ +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': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb new file mode 100644 index 0000000000..337e722e7b --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb new file mode 100644 index 0000000000..58076d4e59 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb @@ -0,0 +1,24 @@ +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': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb new file mode 100644 index 0000000000..6b858f2d9d --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 04bfc4827d82c852f29b1360dc93240de08a80e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:19:37 +0200 Subject: [PATCH 0273/1172] include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works --- .../p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 10 +++++++++- 6 files changed, 54 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb index 2ec3cb1dc8..5c84059a20 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index fdb44db0d0..39d6b11c34 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb index 09917d5025..1e9572eb83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index bb0be0ac85..466ad2cc0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb index 10c6659238..3fafaaa920 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 3950c920d4..5a66cda69a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' -- GitLab From 7e6618a5642325d9039922026ba539a5ff50fce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:27:09 +0200 Subject: [PATCH 0274/1172] use Tk 8.6.3 rather than Tk 8.6.4 as dep in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a.eb | 2 +- .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 2 +- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 ------------------- ...no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} | 2 +- .../t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 24 ++++++++++++++++++ ...X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} | 2 +- 17 files changed, 36 insertions(+), 112 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-GCC-4.9.2-no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-foss-2015.05-no-X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} (97%) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-gompi-1.5.16-no-X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-goolf-1.5.14-no-X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} (97%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index e9840cb7eb..7f438347a5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 0fa5529cb0..d0661c356d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 5eed3b0154..dc26dc666b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 1ff5189a78..cc0e90d0e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 2f9941dfab..ad2c37f79a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 536743d8c5..bb0fac1650 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 499a28228b..d6a4eb1b3c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 71a627c500..ed4d77fc45 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('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 ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb deleted file mode 100644 index fcf9fcc830..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -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': 'GCC', 'version': '4.9.2'} - -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/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb deleted file mode 100644 index a933eab557..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb +++ /dev/null @@ -1,25 +0,0 @@ -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': 'foss', 'version': '2015.05'} - -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/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb deleted file mode 100644 index 099c4a95f4..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb +++ /dev/null @@ -1,25 +0,0 @@ -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': 'gompi', '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' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb deleted file mode 100644 index 150f56cf00..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb +++ /dev/null @@ -1,25 +0,0 @@ -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': 'goolf', 'version': '1.5.14'} - -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-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 3530d74282..602101704a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 337e722e7b..8ff29d34a2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' 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 new file mode 100644 index 0000000000..c34f24fd99 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index 58076d4e59..a292e06eb8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index 6b858f2d9d..cd4da6afb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' -- GitLab From 37f24102612713bb52c192907e11889040d172e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:34:16 +0200 Subject: [PATCH 0275/1172] kbproto is just a build dep --- .../easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb index 778cd1670c..cea866f2b7 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb index fe8ecdca33..80e0f6ea24 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb index 393ccdfa93..52e06388f3 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.7'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.7'), ('libX11', '1.6.3', '-Python-2.7.9'), ] -- GitLab From 6dbc6268d466d2a34aaad21e94b9b5168f25406c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:43:49 +0200 Subject: [PATCH 0276/1172] add missing Tk 8.6.3 intel/2015a easyconfig --- .../t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb 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 new file mode 100644 index 0000000000..d841e7bd84 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From a8b8cd6eeb84d5902bdc13b762b65f95a992f383 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:10:50 +0200 Subject: [PATCH 0277/1172] {data}[intel/2015a] HDF5 1.8.15 --- .../h/HDF5/HDF5-1.8.15-intel-2015a.eb | 27 ++++++ .../h/HDF5/HDF5-1.8.15_configure_intel.patch | 95 +++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb new file mode 100644 index 0000000000..e820f700da --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.15' + +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': '2015a'} +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-%(version)s_configure_intel.patch', + 'configure_libtool.patch', +] + +configopts = "--enable-gpfs" +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch new file mode 100644 index 0000000000..b74e70593e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch @@ -0,0 +1,95 @@ +--- hdf5-1.8.15/configure.orig 2015-05-01 20:56:59.000000000 +0200 ++++ hdf5-1.8.15/configure 2015-06-02 15:04:26.757168623 +0200 +@@ -5190,7 +5190,7 @@ + ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_fc_compiler_gnu + if test -n "$ac_tool_prefix"; then +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5234,7 +5234,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -11993,7 +11993,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc*| ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -12629,11 +12629,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13115,7 +13115,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -16113,7 +16113,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -19024,7 +19024,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc* | ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -19645,11 +19645,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20103,7 +20103,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then -- GitLab From d52f65e1ad073313821ba555c1cfa7d83f6e580c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:42:09 +0200 Subject: [PATCH 0278/1172] drop gpfs versionsuffix and use no longer existing --enable-gpfs configopt for recent HDF5 versions --- ...1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb | 1 - ...-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} | 5 ++--- easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} (92%) rename easybuild/easyconfigs/h/h5py/{h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} (88%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 081c94297d..2b7af38374 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.14' -versionsuffix = '-gpfs' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of @@ -17,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb index e820f700da..9b028b25b8 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -16,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 88% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index d6f4de7c55..665337345c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,12 +17,11 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) +versionsuffix = '-%s-%s%s' % (python, pyver) dependencies = [ (python, pyver), - ('HDF5', '1.8.14', hdf5suff), + ('HDF5', '1.8.14'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 822615186c..baee3155cf 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -20,7 +20,7 @@ patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libctl', '3.2.2'), ('GSL', '1.16'), ('FFTW', '3.3.4') diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index bd7faf3909..0f9bc0fa5f 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.9'), # should have a working sqlite, and provide numpy ('freetype', '2.5.5'), ('LibTIFF', '4.0.4beta'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python -- GitLab From d7c8a53fc9087c0fdaf8c5abffe9330540ad3a50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:55:12 +0200 Subject: [PATCH 0279/1172] fix typo --- .../easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 665337345c..44ec9edf7c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-%s-%s%s' % (python, pyver) +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), -- GitLab From 06f663105c14f3491674941f2cc4101acf93f6c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 16:57:17 +0200 Subject: [PATCH 0280/1172] cURL added as dependency --- easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index cdf98f1940..1931792850 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -21,6 +21,7 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), ('netCDF', '4.3.2') + ('cURL', '7.37.1') ] moduleclass = 'math' -- GitLab From b1d2fff1ebdf73d28a511d6c7d29417d4349507c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:12:20 +0200 Subject: [PATCH 0281/1172] Added external matplotlib dependency and source changed to PYPI --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 7 +++- ...tplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 2 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index 1f11e79748..b9dd51cded 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' @@ -17,7 +17,10 @@ pyshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver -dependencies = [(python, pythonver)] +dependencies = [ + (python, pythonver), + ('matplotlib', '1.3.1'), +] sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..91d3707f42 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.1' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.3'), + ('libpng', '1.6.12'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From a8a944bb018cc966c76271071b87249621bba31b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:19:13 +0200 Subject: [PATCH 0282/1172] toolchain corrected in matplotlib --- .../m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb index 91d3707f42..765f86a131 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ 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': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 6bfc7b9b575209908f2ae661dc2180271d60c315 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:25:50 +0200 Subject: [PATCH 0283/1172] using GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb index 77009b52a1..aef6e26abf 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From 4e6379444e094b0540033f5c84af4a56c197d32b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:43:43 +0200 Subject: [PATCH 0284/1172] versionsuffix added for matplotlib dependency --- .../h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index b9dd51cded..0118dd4b32 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -19,7 +19,7 @@ eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver dependencies = [ (python, pythonver), - ('matplotlib', '1.3.1'), + ('matplotlib', '1.3.1', versionsuffix), ] sanity_check_paths = { -- GitLab From a81ac042848534cce51d17a81c942d378ca67459 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:26:53 +0200 Subject: [PATCH 0285/1172] include checksum + switch to manual download in JUBE easyconfig --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 0044a1ec87..e0a6db9551 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -1,7 +1,7 @@ -easyblock = "VersionIndependentPythonPackage" +easyblock = 'VersionIndependentPythonPackage' -name = "JUBE" -version = "2.0.3" +name = 'JUBE' +version = '2.0.3' homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, @@ -9,8 +9,9 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s sources = [SOURCELOWER_TAR_GZ] +checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} -- GitLab From b2b544310020b5da5d34d5b5baf35ba59b686d5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:27:08 +0200 Subject: [PATCH 0286/1172] add easyconfigs for JUBE 2.0.4 an 2.0.5 --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 23 ++++++++++++++++++++++ easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 23 ++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb new file mode 100644 index 0000000000..dc76af6562 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.4' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96a7946d38d678b25ba4bbd539482a14'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb new file mode 100644 index 0000000000..ea72eb6be6 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.5' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f506e9f39898af3d7456890ba219ab90'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 662aeb0bdca15c55e38160a0249872c94e802cf9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 08:34:47 +0200 Subject: [PATCH 0287/1172] commas corrected --- .../easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index 1931792850..47cf63ba0e 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -20,8 +20,8 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ('netCDF', '4.3.2') - ('cURL', '7.37.1') + ('netCDF', '4.3.2'), + ('cURL', '7.37.1'), ] moduleclass = 'math' -- GitLab From cf66efb4e2461ba170c389924bbb7928fcabadb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:37:53 +0200 Subject: [PATCH 0288/1172] SOURCELOWER -> SOURCE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index e0a6db9551..ffff4a9c2e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index dc76af6562..373d162154 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ea72eb6be6..ebf3c0a914 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] options = {'modulename': 'jube2'} -- GitLab From 4454fbfccee430c04edbba49254539a3b724388a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:01:02 +0200 Subject: [PATCH 0289/1172] Both packages use dependency GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb index 00491cc9ba..270390d86d 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From d3824d539f8d45ed0b2537a3631a4e75dceac622 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:11:24 +0200 Subject: [PATCH 0290/1172] md5schecksum added --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb index 2698ca5e91..920ee4c4fa 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -25,5 +25,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = [('md5', '90b1b8f77313600cc294d9271741f4da')] moduleclass = 'system' -- GitLab From 0c716a66441012c284d71f3bc0a81b70147ac387 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:26:11 +0300 Subject: [PATCH 0291/1172] Fixed config --- .../easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 99d44c6862..79d3f53e5a 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -1,11 +1,12 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'MATIO' version = '1.5.2' @@ -16,10 +17,8 @@ description = """matio is an C library for reading and writing Matlab MAT files. toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] - -dependencies = [('zlib','1.2.7'), -] +dependencies = [('zlib','1.2.7')] moduleclass = 'lib' -- GitLab From a5f4228dc8bc378fe248f5d9b86c1dd5a6c64750 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:43:11 +0300 Subject: [PATCH 0292/1172] Fixes in easyconfig --- .../DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb index d3ec591256..2734b69ecf 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -7,19 +7,20 @@ # $Id$ # ## - easyblock = "PythonPackage" name = 'DendroPy' version = '3.12.0' homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. -""" +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] -sources = ['%s-%s.tar.gz' % (name, version)] +sources = [SOURCE_TAR_GZ] python = "Python" pythonversion = '2.7.3' @@ -30,7 +31,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', + 'bin/sumtrees.py','bin/strict_consensus_merge.py'], 'dirs': [], } -- GitLab From b684e5971fa21996893a2a3be3e4d2d3a292f2c6 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 09:52:28 +0200 Subject: [PATCH 0293/1172] renamed to MuTect and updated download url --- ...t-1.1.4-Java-1.7.0_76.eb => MuTect-1.1.4-Java-1.7.0_76.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/MuTect/{muTect-1.1.4-Java-1.7.0_76.eb => MuTect-1.1.4-Java-1.7.0_76.eb} (94%) diff --git a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb similarity index 94% rename from easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb rename to easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index ee2805d464..2a8458e2e5 100644 --- a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -5,7 +5,7 @@ easyblock = 'Tarball' -name = 'muTect' +name = 'MuTect' version = '1.1.4' homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' @@ -16,7 +16,7 @@ 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/'] -sources = ['%(name)s-%(version)s-bin.zip'] +sources = ['muTect-%(version)s-bin.zip'] java = 'Java' javaver = '1.7.0_76' -- GitLab From 3027f180c35a32b5289a5ed0b669c5d95e5a9915 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 09:58:57 +0200 Subject: [PATCH 0294/1172] add source_urls using download.php?file= --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index ffff4a9c2e..2803f111f1 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 373d162154..31b888866e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ebf3c0a914..4313248d99 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 283908c4c27cc74b3b44d5d4499ee76aaffd8826 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 10:02:36 +0200 Subject: [PATCH 0295/1172] fix typo --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 2803f111f1..903be570eb 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 31b888866e..545b5785ea 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index 4313248d99..b270f53d57 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 884bc004100e2103387e49640296ab011510c3e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:12:07 +0200 Subject: [PATCH 0296/1172] use autotools --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index c3b27fffcb..43293cbe1d 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autoconf', '2.69')] +builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 1df688fd2a9832a2b272060ed4e14c35680005ae Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:18:49 +0200 Subject: [PATCH 0297/1172] correct version --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index 43293cbe1d..c4afd6154b 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 03a20f0bcdfefa678a34e5a201eda032b944b7b4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:33:48 +0300 Subject: [PATCH 0298/1172] Changes in config file --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index d749578a18..beb147df02 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -6,30 +6,26 @@ # License:: MIT/GPL # ## - easyblock = "Tarball" name = 'Bismark' version = '0.10.1' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' -description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" +description = """A tool to map bisulfite converted sequence reads and +determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] - -dependencies = [ - ('Bowtie2', '2.0.2'), -] +dependencies = [('Bowtie2', '2.0.2')] sanity_check_paths = { - 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], 'dirs': [], } -modextrapaths = {'PATH': ''} - moduleclass = 'bio' -- GitLab From 91aa792c2defe803b961a11f29f81ca5540bf6a8 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:45:23 +0300 Subject: [PATCH 0299/1172] removing ABINIT files; bismark branch --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 ------------------- .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ---------------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 -------------- 3 files changed, 99 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb delete mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb deleted file mode 100644 index a3fe29c410..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ABINIT' -version = '7.4.3' - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing - condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = ['%s-%s.tar.gz' % (name.lower(), version)] -source_urls = ['http://ftp.abinit.org/'] - -configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' -configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' -configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' - -dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), -] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb deleted file mode 100644 index fb4d81965f..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb +++ /dev/null @@ -1,32 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -easyblock = "Tarball" - -name = 'ABINIT' -version = '7.4.3' -versionsuffix = '-x86_64_linux_gnu4.5' - -altversions = ['7.0.3', '7.0.4', '7.0.5'] - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] -source_urls = ['http://ftp.abinit.org/'] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb deleted file mode 100644 index 350da2d908..0000000000 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ /dev/null @@ -1,29 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ETSF_IO' -version = '1.0.4' - -homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] - -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" - -dependencies = [ ('netCDF', '4.1.3') ] - -sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } - -moduleclass = 'chem' -- GitLab From 27381d2c985988915b21e13302101816a61ed6a3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 10:47:17 +0200 Subject: [PATCH 0300/1172] using separate python module --- ...uitscape-4.0.5-intel-2014b-Python-2.7.8.eb | 1 + .../PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 31 +++++++++++++++++++ .../p/Python/Python-2.7.8-intel-2014b.eb | 31 ++++++++++--------- 3 files changed, 48 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb index a07b1584dc..b2653a8675 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -23,6 +23,7 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), + ('PyAMG', '2.2.1', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..0bbb1b820f --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '2.2.1' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.8' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pyamg' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 76a6bcb647..787f5ecab1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -22,19 +22,22 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + # order is important! # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - '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')], @@ -46,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['https://mpi4py.googlecode.com/files/'], + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -63,9 +66,12 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + '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/'], @@ -81,20 +87,15 @@ exts_list = [ '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', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), ('pyparsing', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), - ('matplotlib', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], - }), - ('pyamg', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyamg/'], - }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] - moduleclass = 'lang' -- GitLab From e486daf541a839a09ff57dd7ee0eb0f0ee462421 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 10:56:59 +0200 Subject: [PATCH 0301/1172] trial to remove Python modifications --- .../p/Python/Python-2.7.8-intel-2014b.eb | 28 ++++++++----------- 1 file changed, 12 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 787f5ecab1..fc03cf9418 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -22,22 +22,19 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - # order is important! # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +46,13 @@ exts_list = [ '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/'], + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://mpi4py.googlecode.com/files/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -66,12 +63,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), - ('six', '1.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -87,15 +81,17 @@ exts_list = [ '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', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), ('pyparsing', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('matplotlib', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' -- GitLab From 8550a555814b6331d8193536a75e6ac41672181c Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:05:35 +0300 Subject: [PATCH 0302/1172] Fixing source_url --- easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index beb147df02..337980614f 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] dependencies = [('Bowtie2', '2.0.2')] -- GitLab From e6e6f48a7a4693953e8bb38614d4b52bc3950877 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:18:02 +0200 Subject: [PATCH 0303/1172] synced with current develop, foss/2015a version updated --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb index 8319de8066..e42de69332 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] -- GitLab From 3a8ac4416f6863c307ee4d585d749cc355853ab0 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:18:14 +0300 Subject: [PATCH 0304/1172] Fixed configs according to comments --- ...BINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} | 23 +++++++++++-------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 21 +++++++++++------ 2 files changed, 28 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-7.4.3-goolf-1.4.10.eb => ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} (59%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb similarity index 59% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb index c1d2b559d8..4d319523ac 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -1,35 +1,40 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = "ConfigureMake" name = 'ABINIT' version = '7.4.3' +versionsuffix = '-ETSF_IO-1.0.4' homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), ] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index 7e1b945d47..f270612d5f 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -1,27 +1,34 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'ETSF_IO' version = '1.0.4' homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" dependencies = [ ('netCDF', '4.1.3') ] sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } + 'files': ["bin/etsf_io"], + 'dirs': [] +} +moduleclass = 'lib' -- GitLab From 5c634f7678d0ae2e66f3b90f1b384d507c190e40 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:23:58 +0200 Subject: [PATCH 0305/1172] sourceLOWER added --- .../p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb index 0bbb1b820f..360297f0ce 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -8,8 +8,8 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCELOWER] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.8' -- GitLab From 00f7b94da182e20d1ed4b8d80ef20e768459e095 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:32:41 +0200 Subject: [PATCH 0306/1172] PYPI_LOWER_SOURCE fixed --- .../easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb index 360297f0ce..44847179db 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = [PYPI_SOURCELOWER] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -- GitLab From bfe7601591b4c8c24c965692748dcae63dd63a5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 11:52:30 +0200 Subject: [PATCH 0307/1172] include MD5sum for CUDA 6.0.37 source file --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index 0ebf372eeb..76cb0b94f9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -24,5 +24,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = ['22f50793b6704fe987983302fa7d1707'] moduleclass = 'system' -- GitLab From ee063ccdefc5305aeb3e36a04ff0dd03f5f0a6ee Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 12:03:40 +0200 Subject: [PATCH 0308/1172] - Pango-1.36.7-intel-2014b.eb : added missing dependency ('libXft', '2.3.2') because of sanity check --- easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index eba092fa74..1de69091f3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -22,6 +22,7 @@ dependencies = [ ('GLib', '2.40.0'), ('HarfBuzz', '0.9.35'), ('GObject-Introspection', '1.42.0'), + ('libXft', '2.3.2'), ] builddependencies = [ -- GitLab From fc0c5c7a197088ae823d7c208dc8b4c420db129f Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 12:08:11 +0200 Subject: [PATCH 0309/1172] - Qt-4.8.6-intel-2014b.eb : updated source_urls --- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935..b87b87bd72 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -7,8 +7,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] -- GitLab From cca6949bb0f836117e65778687b65bca1b088743 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 12:21:32 +0200 Subject: [PATCH 0310/1172] CGAL comments removed --- .../easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb | 3 --- .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb index 1eb2d83747..4545d7456c 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb @@ -10,8 +10,6 @@ toolchainopts = {'strict': True} sources = [SOURCE_TAR_BZ2] source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] -# The directory changes with the version (and maybe in time) ---^ -# Have to accept license agreement pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion @@ -28,4 +26,3 @@ builddeps = [ ] moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index 374c22547b..f2b18cd866 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -10,8 +10,6 @@ toolchainopts = {'strict': True} sources = [SOURCE_TAR_BZ2] source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] -# The directory changes with the version (and maybe in time) ---^ -# Have to accept license agreement pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion @@ -28,4 +26,3 @@ builddeps = [ ] moduleclass = 'numlib' - -- GitLab From ed27a09ec26e06e4a07bd257e6f3705ffb427c89 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 26 Mar 2014 15:52:55 +0100 Subject: [PATCH 0311/1172] fixed ECore easyconfigs and dependencies, since it simply doesn't work with a openmpi built with gcc --- .../e/ECore/ECore-1.5.2-clusterapps.eb | 4 +- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 3 +- .../h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 17 ++++++++ .../o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 39 +++++++++++++++++++ 4 files changed, 59 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb index 526f2442cd..6bfb37241d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb @@ -13,8 +13,8 @@ sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +# needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 +dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index 382a1b327e..dd16f0a9f1 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,8 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +dependencies = [('OpenMPI', '1.4.5', 'ictce', '5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..884dc745a7 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = "1.7.2" + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..f65c7d844b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +name = 'OpenMPI' +version = "1.4.5" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69'), +] + +dependencies = [('hwloc', '1.7.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +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-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "open-pal", "open-rte"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 45e3c80bc1eac0c18c835964f6ea8b2af9a523d3 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 3 Apr 2014 11:02:16 +0200 Subject: [PATCH 0312/1172] fixed wrong suffix --- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index dd16f0a9f1..ce44a8981d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', 'ictce', '5.5.0')] +dependencies = [('OpenMPI', '1.4.5', 'ictce-5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From 19981e5adc20b2a545d5b1612d1d3ba7dd8c6dac Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 3 Apr 2014 11:10:44 +0200 Subject: [PATCH 0313/1172] another typo fix in toolchain version --- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index ce44a8981d..5e6f6b0b1c 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', 'ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From 171f98c6ee423731fce8b2d7468181131b0b28e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:25:01 +0200 Subject: [PATCH 0314/1172] fix ncurses patch for v5.9-20130406 --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 2 +- .../ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 2 +- .../ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 2 +- .../ncurses-5.9-20130406_configure_darwin.patch | 11 +++++++++++ 8 files changed, 18 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 6d40fe65a5..634fda5b4d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 7d2df71a8f..4f21474dcf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index a971bf0cc9..a71c6aab72 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 360335ba07..f2a6bbb76a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 021bbd904f..5ef3e822ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 439c4ca406..96cc600747 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 1fcb38e69b..a1409a10e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch new file mode 100644 index 0000000000..067ec128f9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch @@ -0,0 +1,11 @@ +--- ncurses-5.9-20130406/configure.orig 2013-04-07 00:09:21.000000000 +0200 ++++ ncurses-5.9-20130406/configure 2015-06-03 12:20:33.765043843 +0200 +@@ -5587,7 +5587,7 @@ + chmod +x mk_shared_lib.sh + ;; + darwin*) #(vi +- cf_try_cflags="no-cpp-precomp" ++ #cf_try_cflags="no-cpp-precomp" + CC_SHARED_OPTS="-dynamic" + MK_SHARED_LIB='${CC} ${CFLAGS} -dynamiclib -install_name ${libdir}/`basename $@` -compatibility_version ${ABI_VERSION} -current_version ${ABI_VERSION} -o $@' + test "$cf_cv_shlib_version" = auto && cf_cv_shlib_version=abi -- GitLab From e8952f17f155a4029f7ed8fbe4e11854e62cd493 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 24 Sep 2014 13:25:46 +0200 Subject: [PATCH 0315/1172] added paraview for intel-2014b --- .../g/GLib/GLib-2.41.2-intel-2014b.eb | 18 +++++++++++++++ .../p/Paraview/Paraview-4.1.0-intel-2014b.eb | 22 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb create mode 100644 easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb new file mode 100644 index 0000000000..23fc05daec --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -0,0 +1,18 @@ +name = 'GLib' +version = '2.41.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" +toolchain = {'name': 'intel', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.8')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb new file mode 100644 index 0000000000..2f704c2b24 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'Paraview' +version = '4.1.0' + +homepage = "http://www.paraview.org" +description = "Paraview is a scientific parallel visualizer" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'usempi': False, 'pic': True} + +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"] + +dependencies = [('Qt','4.8.6')] + +builddependencies = [('CMake', '3.0.0')] + +separate_build_dir = True + +moduleclass = 'vis' -- GitLab From 910656a9c7a0b3cbcb1684970a8a06c0ba81ba07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:35:05 +0200 Subject: [PATCH 0316/1172] use %(version)s rather than hardcoding 5.9 in ncurses patch specs --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 4 +--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 2 +- 33 files changed, 33 insertions(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 399dc72d43..37a2fff35a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index bcf8a1dcfa..96e1f45472 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index d967731cf4..5dd295c39e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 9608f82f81..3071876ad2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -8,15 +8,13 @@ description = """The Ncurses (new curses) library is a free software emulation o 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.""" -patches = ['ncurses-5.9_configure_darwin.patch'] - toolchain = {'name': 'GCC', 'version': '4.8.2'} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 6bf4c2b332..c5e4c7e93d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 6313c884fc..5125329966 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 727175a0e9..7278bb4ccf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 26e6ab54bf..cff4af273d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index c993267096..b529181479 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 38361f94f7..aaa5b2bd78 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index b057182b0c..f8ee92d094 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index d67bdf2770..9936cdbc6c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 169534ccd8..b5428d27b0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 7e1f5ce19f..21128a21c5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 2df180dac8..fa8d19afbb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index c31fdc08ca..cdf8cdb5ce 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index bfba6b87fe..36b5053e62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 76b20bd13a..292cec33e2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 1cb1b2fa6b..0b4bbba9ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index cf54b65a18..b5099d8795 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 7ee6110e8d..94e44f7817 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 5753a19c6f..b1c1a88d75 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 7466ea8529..fed58a89dd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 2df3b61306..bf996a362f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 0d8611a193..671b5796ac 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index ce62d53ca0..61118f9005 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 017c395992..278cc8d64a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index b6a67863ad..38c7d07988 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index edb943229c..9fa751952c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 4912fd41da..24097805bc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 389a334b0b..115d1bd981 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index ab5729d6df..e4351873f4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 1a23dd3813..529b47259f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build -- GitLab From d9b6f0b5ffa86dbf02905755cf4b574476c43ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:41:11 +0200 Subject: [PATCH 0317/1172] sync ncurses easyconfigs --- .../n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 19 ++++++++++++++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 20 ++++++++++++++--- .../n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 21 ++++++++++++++++++ .../n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 21 ++++++++++++++++++ .../n/ncurses/ncurses-5.9-intel-2014.06.eb | 21 ++++++++++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9.eb | 21 ++++++++++++++++++ 9 files changed, 174 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 23ac2489aa..0683b0f7a3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/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/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 95c1010bbc..6cb29748e3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/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/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index af63de1cff..96517f4a7a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/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/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 946a1c5338..a769a56170 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -14,4 +14,23 @@ 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/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 3ab27d3a62..37d7e04809 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,11 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/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/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index 9f6619baca..e272a823d6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ 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/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb index a62ac8f668..9a1708ba34 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ 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/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb index e1045e7b9f..d67fc45cbf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ 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/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 6ab79de61f..dd70b0800a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ 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' -- GitLab From dab59113ad43a5ee0a40449487138c7a24ec2e0e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:45:01 +0200 Subject: [PATCH 0318/1172] fixed remarks --- .../easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 16f1a1e3ae..8acfc38319 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -11,15 +11,15 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +source_urls = ['SOURCEFORGE_SOURCE'] -dependencies = [ - ('Bison', '3.0.2'), - ('flex', '2.5.39'), +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), ] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], - 'dirs': [], + 'dirs': [], } moduleclass = 'cae' -- GitLab From 5264f8e1bf6be28dffd88d0ccfa62c3e9a107dbb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:50:00 +0200 Subject: [PATCH 0319/1172] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb index 884dc745a7..c914d40121 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'hwloc' version = "1.7.2" @@ -10,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index f65c7d844b..5b5a80e895 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'OpenMPI' version = "1.4.5" -- GitLab From 32c3812fe39fd9171d66a5d0b13330aec2cde43f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:54:03 +0200 Subject: [PATCH 0320/1172] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index 23fc05daec..f3e83d90ac 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'GLib' version = '2.41.2' -- GitLab From bc620c3f35a0b7373e13feb920ff66560f942ba6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:58:49 +0200 Subject: [PATCH 0321/1172] enable 'shared' tcopt in ncurses Cray easyconfigs --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 0683b0f7a3..6b7bb1c347 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 6cb29748e3..01680ab5b7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index 96517f4a7a..6f00fdbd51 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From 6dfc9321176f7a2132b7018132623a9bdccd9d9f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:16:07 +0200 Subject: [PATCH 0322/1172] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 8acfc38319..942515bb81 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'ngspice' version = '26' -- GitLab From dcdc87c8a8fb10c283eb2d3d6dae7ee37f5ab3ff Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:18:42 +0200 Subject: [PATCH 0323/1172] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb index c914d40121..1f891126fd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'hwloc' version = "1.7.2" diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 5b5a80e895..585ea11236 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.4.5" -- GitLab From 5a247ac0ebf67be5b8a49c97280a9143f94a26a8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:20:19 +0200 Subject: [PATCH 0324/1172] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index f3e83d90ac..cec860f2de 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GLib' version = '2.41.2' -- GitLab From b74af28326bb0c4850578ab7a4cec1b59bb73de1 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:28:46 +0200 Subject: [PATCH 0325/1172] fixed tecplot ec name 6 remarks --- .../t/tecplot360ex/tecplot-360ex.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb new file mode 100644 index 0000000000..08531bb3f3 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' -- GitLab From 20ca4139b6f20a4317666ed82ff4f48c91ccb19e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:32:05 +0200 Subject: [PATCH 0326/1172] fixed remarks --- .../easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 13 +++++++------ .../easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 10 ++++++++-- 2 files changed, 15 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 175efc7a74..4ed102f04a 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -2,14 +2,15 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'tabix' version = '0.2.6' homepage = 'http://samtools.sourceforge.net' -description = """ Generic indexer for TAB-delimited genome position files """ +description = """ Generic indexer for TAB-delimited genome position files """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -21,12 +22,12 @@ dependencies = [('zlib', '1.2.8')] files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), - "example.gtf.gz", + "example.gtf.gz", "example.gtf.gz.tbi", - "NEWS", + "NEWS", "ChangeLog" -] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 2f4bddea4e..8e12dc4f34 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,4 +1,10 @@ -easyblock='MakeCp' +# 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 +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' name = 'tabix' version = '0.2.6' @@ -20,7 +26,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From 1c74b575fa8e499af1f7057ff847af3c6736b844 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:33:03 +0200 Subject: [PATCH 0327/1172] makeopts -> buildopts --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 4ed102f04a..808db8594a 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -27,7 +27,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 8e12dc4f34..f364f9fafd 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,4 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +pts # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel @@ -26,7 +27,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From a43ea9539a862566d62ba036b152a5e05d6a6662 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 14:33:35 +0300 Subject: [PATCH 0328/1172] Fixes after review --- .../easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 10 +++++++--- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 4661417502..2060e3874c 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -1,18 +1,19 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' description = """Program proj is a standard Unix filter function which converts - geographic longitude and latitude coordinates into cartesian coordinates""" +geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -21,6 +22,9 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], 'dirs': [], } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 589656723f..427477bf96 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -1,18 +1,19 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' description = """Program proj is a standard Unix filter function which converts - geographic longitude and latitude coordinates into cartesian coordinates""" +geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -21,6 +22,9 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], 'dirs': [], } + +moduleclass = 'lib' -- GitLab From 301b11ffb83d864cb71f2bc4cd08cef67fc62e91 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:33:58 +0200 Subject: [PATCH 0329/1172] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 942515bb81..d22d8136b3 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'ngspice' version = '26' -- GitLab From dfd5a4cd444ffd206e1007be32d805e8e3b16282 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:43:29 +0200 Subject: [PATCH 0330/1172] fixed osdependencies for OpenMPI --- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 585ea11236..c793f86806 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -24,11 +24,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + -- GitLab From f9fdbd6119398a606825ce7b0637be5e32e43120 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 14:44:08 +0300 Subject: [PATCH 0331/1172] Style Fixes --- .../Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 16 +++++++--------- .../Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 17 +++++++---------- 2 files changed, 14 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb index 8308ab148a..28482a1b30 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,8 +4,8 @@ name = 'Theano' version = '0.6.0' homepage = 'http://deeplearning.net/software/theano' -description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions -involving multi-dimensional arrays efficiently.""" +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -17,14 +17,12 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -dependencies = [ - (python, pythonver), - ] +dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], - 'dirs': [] - } + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb index 1e72223824..e95fac6936 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,9 +4,8 @@ name = 'Theano' version = '0.6.0' homepage = 'http://deeplearning.net/software/theano' -description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions - involving multi-dimensional arrays efficiently.""" - +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} @@ -18,14 +17,12 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -dependencies = [ - (python, pythonver), - ] +dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], - 'dirs': [] - } + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} moduleclass = 'math' -- GitLab From 2730bfd14d00b9cb9bb465eceb7570cf6af1a77d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 13:51:17 +0200 Subject: [PATCH 0332/1172] Revert "Delete imkl-10.3.12.361.eb" This reverts commit 7f2076dcc517dcac3b51742cc86ddb20cc274adf. --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb new file mode 100644 index 0000000000..dfb97e3568 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -0,0 +1,29 @@ +name = 'imkl' +version = '10.3.12.361' + +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': 'dummy', 'version': 'dummy'} + +sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] + +# deps for interface build +dependencies = [ + ('icc', '2011.13.367'), + ('ifort', '2011.13.367'), + ('impi', '4.1.0.027'), +] + +dontcreateinstalldir = 'True' + +interfaces = True + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'numlib' -- GitLab From d0ecabf99cf121127f2095ccb938843ad648fa67 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 13:52:03 +0200 Subject: [PATCH 0333/1172] Revert "Delete impi-4.1.0.027.eb" This reverts commit 83ac4560b153fbadb3103c3cfb7b7efdb3691444. --- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb new file mode 100644 index 0000000000..d074eeb0ea --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.0.027' + +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': 'dummy', 'version': 'dummy'} + +sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 29c3488210050842cfab67fb62b7f859c789e6c5 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 Aug 2014 10:42:48 +0200 Subject: [PATCH 0334/1172] Don't run the Bloom tests for Jellyfish, they can randomly fail --- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df..e874c05030 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" sanity_check_paths = { 'files': ['bin/jellyfish'], -- GitLab From 59f614145445bd94c9dc18e8b420ef491e8a387e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:57:55 +0200 Subject: [PATCH 0335/1172] removed bad easyconfig --- .../t/tecplot360ex/tecplot360ex.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb deleted file mode 100644 index 08d437e5b8..0000000000 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Binary' - -name = 'tecplot360ex' -version = 'linux64' - -homepage = 'http://www.tecplot.com/' -description = """ - Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, - and communicate your results with professional images and animations. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# fi. http://www.tecplot.com/my/product-releases/ -installername = '%(name)s_%(version)s.sh' -sources = [installername] - -sanity_check_paths = { - 'files': ['bin/tec360'], - 'dirs': [] -} -install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) -moduleclass = 'vis' - -- GitLab From a80d2cd20acb2b51dde642f34c292967a9f8017e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:01:24 +0200 Subject: [PATCH 0336/1172] Fixed intermittent modifications after revert --- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 8 +++++--- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index dfb97e3568..0db4c8f64f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,12 +9,14 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] +sources = ['l_mkl_%(version)s.tgz'] + +compver = '2011.13.367' # deps for interface build dependencies = [ - ('icc', '2011.13.367'), - ('ifort', '2011.13.367'), + ('icc', compver), + ('ifort', compver), ('impi', '4.1.0.027'), ] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index d074eeb0ea..839fe8f604 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] +sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' -- GitLab From 273386ca814a34da61bd54d5860de661d4a91f4b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:09:27 +0200 Subject: [PATCH 0337/1172] Use %(version)s as suggested --- easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 e4a2454e0e..0b93b9c580 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 @@ -16,7 +16,7 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" -sources = ['binutils-%s.tar.bz2' % version] +sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.5.14'} -- GitLab From 21a0a26dae34726e73e5e9330a6fde4f04eae2f4 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:21:31 +0200 Subject: [PATCH 0338/1172] Updated easyconfigs --- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 8 +++++--- .../easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 10 +++++++--- .../easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 2 ++ .../easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb | 2 ++ 5 files changed, 18 insertions(+), 6 deletions(-) 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 0b93b9c580..1922cb5d12 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 @@ -10,18 +10,20 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## +easyblock = 'ConfigureMake' + name = 'binutils' version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" -sources = ['binutils-%(version)s.tar.bz2'] -source_urls = [GNU_SOURCE] - toolchain = {'name': 'goolf', 'version': '1.5.14'} 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 = { diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index 3628401ad4..b4f0251684 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -17,13 +18,16 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'goolf', 'version': '1.5.14'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] dependencies = [('Qt', '4.8.4')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index c2bd8f4970..9e66f41f61 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -3,6 +3,8 @@ # License:: New BSD # ## +easyblock = 'ConfigureMake' + name = "OPARI2" version = "1.1.2" diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb index f1dcf6fbfe..d485c2eb57 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## +easyblock = 'ConfigureMake' + name = 'PAPI' version = '5.2.0' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb index 1933e4066b..85a3447e47 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -3,6 +3,8 @@ # License:: New BSD # ## +easyblock = 'ConfigureMake' + name = "PDT" version = "3.20" -- GitLab From c5df41c24c550dd9ddb29ba8cd61e3f1ad615442 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:24:22 +0200 Subject: [PATCH 0339/1172] Cosmetics --- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index 9e66f41f61..34e2fdbcea 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'ConfigureMake' name = "OPARI2" diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index e0a03c63d3..60c9ce8691 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -6,6 +6,7 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "OTF2" diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb index 85a3447e47..bb1e979e80 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'ConfigureMake' name = "PDT" diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index 196dc0e191..137bacee9c 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # # make sure we don't fall back to the ConfigureMake easyblock + easyblock = 'EB_Score_minus_P' name = "Score-P" -- GitLab From 01fe2f370f5b7e04aac75a9f2f30317be57732a3 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 3 Jun 2015 08:42:36 -0400 Subject: [PATCH 0340/1172] adding the easyblock for ConfigureMake --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb index bbe68cc575..b307dca6af 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'BCFtools' version = '1.1' -- GitLab From 5eec0de784d331e48c3c0b17d232813a4357e777 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 15:06:14 +0200 Subject: [PATCH 0341/1172] remove outdated comment --- easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb index c9ba2ffbaf..cbf18980bc 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -24,7 +24,6 @@ description = """PAPI provides the tool designer and application engineer with a 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] -- GitLab From c9dc018ba771899d25cc843d23bda87e3e67e52d Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 15:31:15 +0200 Subject: [PATCH 0342/1172] - Perl-5.20.0-intel-2014b.eb : added some extensions (needed for SOBA) --- .../p/Perl/Perl-5.20.0-intel-2014b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index 197f8c762a..afa1c420a1 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -812,6 +812,59 @@ exts_list = [ 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB/'], }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/S/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ] moduleclass = 'lang' -- GitLab From cad86d34fcb09fa830f307891fd476103dc03db5 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:33:29 +0200 Subject: [PATCH 0343/1172] fixed sanity check and message on load --- easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index 2a8458e2e5..afe163b841 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -25,12 +25,12 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] sanity_check_paths = { - 'files': ["%(name)s-%(version)s.jar"], + 'files': ["muTect-%(version)s.jar"], 'dirs': [], } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/%(name)s-%(version)s.jar +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' -- GitLab From cac43dea05551c515ca2c0b8207bf3f53d22d274 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 15:35:49 +0200 Subject: [PATCH 0344/1172] - GraphViz-2.18-intel-2014b-Perl-5.20.0.eb : new Perl interface to Graphviz --- .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..a7968a4929 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'GraphViz' +version = '2.18' + +homepage = 'https://metacpan.org/pod/GraphViz' +description = """This module provides a Perl interface to the amazing Graphviz, +an open source graph visualization tool from AT&T.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] +sources = [SOURCE_TGZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("Graphviz", "2.38.0"), +] + + +options = {'modulename': 'GraphViz'} + +moduleclass = 'vis' -- GitLab From 5ec08a68cbf58b8727cc084c1089a72832f62e8c Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:46:24 +0200 Subject: [PATCH 0345/1172] fixed typo --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index f364f9fafd..cc5cb2cc40 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,5 +1,4 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -pts # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -- GitLab From 7f8021baaefe768dfe0dd0cd0f91c64547b21a41 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 Aug 2014 10:42:48 +0200 Subject: [PATCH 0346/1172] Don't run the Bloom tests for Jellyfish, they can randomly fail --- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df..e874c05030 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" sanity_check_paths = { 'files': ['bin/jellyfish'], -- GitLab From 4b4938bf43a2cd2d95964ba82d29e7c449352f6b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 17:35:04 +0200 Subject: [PATCH 0347/1172] added sailfish, uses c++11, so no full intel support yet --- .../g/g2log/g2log-1.0-foss-2014b.eb | 27 +++++++++++++++ .../Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 34 +++++++++++++++++++ .../s/Sailfish/Sailfish-0.6.3-foss-2014b.eb | 30 ++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb new file mode 100644 index 0000000000..3ea56b7193 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -0,0 +1,27 @@ +name = 'g2log' +version = '1.0' +easyblock = 'CMakeMake' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.0.0'), +] + +start_dir = 'g2log' +parallel = 1 +moduleclass = 'devel' + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..b8fe958616 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,34 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), + ('Jellyfish', '2.1.3'), + ('g2log', '1.0'), +] + +preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb new file mode 100644 index 0000000000..25da9fbb78 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb @@ -0,0 +1,30 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('binutils', '2.24'), + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +moduleclass = 'bio' -- GitLab From 3bae85691d97cd62241c3e09d8071c4146d6bb70 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 26 Aug 2014 15:37:04 +0200 Subject: [PATCH 0348/1172] added missing dependencies --- .../Boost-1.55.0-foss-2014b-Python-2.7.8.eb | 26 +++++++++++++++++++ .../c/CMake/CMake-2.8.12-foss-2014b.eb | 20 ++++++++++++++ .../j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 26 +++++++++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..8d26308267 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb new file mode 100644 index 0000000000..9aa6ac6517 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': '2014b'} + +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' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb new file mode 100644 index 0000000000..1adc72b8e1 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -0,0 +1,26 @@ +# 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 = 'Jellyfish' +version = '2.1.3' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" +toolchain = {'name': 'foss', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 9d5284b392acf12a14e987cc4d8caa6120b2f6e5 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 13:28:07 +0100 Subject: [PATCH 0349/1172] removed unwanted easyconfig --- .../s/Sailfish/Sailfish-0.6.3-foss-2014b.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb deleted file mode 100644 index 25da9fbb78..0000000000 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'Sailfish' -version = '0.6.3' -easyblock = 'CMakeMake' - -homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' -description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of - isoform abundances directly from a set of reference sequences and RNA-seq reads. """ - -toolchain = {'name': 'foss', 'version': '2014b'} - -source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] -sources = ['v%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.8' -versionsuffix = '-%s-%s' % (python, pyver) - -builddependencies = [ - ('binutils', '2.24'), - ('CMake', '3.0.0'), -] - -dependencies = [ - ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', True), -] - -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" - -moduleclass = 'bio' -- GitLab From 64eeafd8c47ba44fdb4cec5fa114242187563193 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 13:29:41 +0100 Subject: [PATCH 0350/1172] fixed remarks --- easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb | 3 ++- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb index 3ea56b7193..342cbc03cb 100644 --- a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -19,9 +19,10 @@ builddependencies = [ start_dir = 'g2log' parallel = 1 -moduleclass = 'devel' sanity_check_paths = { 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], 'dirs': [], } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb index 1adc72b8e1..10823b3f36 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -8,7 +8,8 @@ version = '2.1.3' homepage = 'http://www.genome.umd.edu/jellyfish.html' description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" -toolchain = {'name': 'foss', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) + +toolchain = {'name': 'foss', 'version': '2014b'} source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 4066e7c7762d37c1308a540b62d8a3fb9242a1ea Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 14:56:01 +0100 Subject: [PATCH 0351/1172] added ConfigureMake where needed --- easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb | 2 ++ easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 1 + 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb index 9aa6ac6517..08b9903802 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CMake' version = '2.8.12' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb index 10823b3f36..bd77b8e773 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -2,6 +2,7 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' name = 'Jellyfish' version = '2.1.3' -- GitLab From 34cce2fcad0621644e950ac0c88815d14baf1293 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:52:55 +0200 Subject: [PATCH 0352/1172] added CMake 3.0.0-foss-2014b --- .../c/CMake/CMake-3.0.0-foss-2014b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000..afa437e164 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '3.0.0' + +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': 'foss', 'version': '2014b'} + +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' -- GitLab From fe7b8fd78399f80a849e1bdc0fcb3a97672369fe Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:19:42 +0200 Subject: [PATCH 0353/1172] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb index afa437e164..872f8b4d7d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CMake' version = '3.0.0' -- GitLab From 7ac3150de254be2566bf5ca87bab84e3eebb0063 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:48:36 +0200 Subject: [PATCH 0354/1172] style fixes in boost easyconfig --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index fa03c1c2ae..52215bc3eb 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -14,9 +14,9 @@ dependencies = [('bzip2', '1.0.6')] osdependencies = [('zlib-devel','zlib1g-dev')] +configopts = '--without-libraries=python' + # also build boost_mpi boost_mpi = True -configopts = '--without-libraries=python' - moduleclass = 'devel' -- GitLab From be89f2ec2da4ba5a4255869e8732cfd60707b5f0 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:49:46 +0200 Subject: [PATCH 0355/1172] use template %(version)s for patch name --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index 2a4b09be4d..d99d70b100 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -17,7 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] -patches = ['tophat-2.0.13-zlib.patch'] +patches = ['tophat-%(version)s-zlib.patch'] dependencies = [ ('Boost', '1.55.0'), -- GitLab From d7d3960d550a8bd345369795efcd6d9cf6db7ef0 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:51:24 +0200 Subject: [PATCH 0356/1172] added zlib as eb dependency instead of system dep --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 52215bc3eb..644fd26b38 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -10,9 +10,9 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] -dependencies = [('bzip2', '1.0.6')] - -osdependencies = [('zlib-devel','zlib1g-dev')] +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8')] configopts = '--without-libraries=python' -- GitLab From e39d1aa90b59708d7ef5be81b46695b6d77262d0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 3 Jun 2015 09:52:18 -0400 Subject: [PATCH 0357/1172] moved deps up under source_urls --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 12 ++++++------ easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) 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 ceec29fe23..6a03e95dba 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 @@ -25,12 +25,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -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=${EBPERLROOT} --enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), @@ -38,6 +32,12 @@ dependencies = [ ('Perl', '5.20.1', '-bare'), ] +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb index d03af57112..ec7ac4488b 100644 --- a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb @@ -25,12 +25,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -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=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), @@ -38,6 +32,12 @@ dependencies = [ ('Perl', '5.20.1', '-bare'), ] +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], -- GitLab From 2d6731ed2480805eb6a25d63835d79472bd830dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 15:53:10 +0200 Subject: [PATCH 0358/1172] update blasr easyconfig & fix style issues --- .../b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb | 43 --------------- .../blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 52 +++++++++++++++++++ ...> blasr-smrtanalysis-2.1_non-static.patch} | 0 3 files changed, 52 insertions(+), 43 deletions(-) delete mode 100644 easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb rename easybuild/easyconfigs/b/blasr/{non-static.patch => blasr-smrtanalysis-2.1_non-static.patch} (100%) diff --git a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb deleted file mode 100644 index 5663de6022..0000000000 --- a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb +++ /dev/null @@ -1,43 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for BLASR: -# ---------------------------------------------------------------------------- -# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Petar Forai -# ---------------------------------------------------------------------------- - -name = 'blasr' -version = 'smrtanalysis-2.1' - -easyblock = "MakeCp" - -homepage = 'https://github.com/PacificBiosciences/blasr' -description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" - - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} - -#like https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz for tag smnrtanalysis -sources = ['%(version)s.tar.gz'] -source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] - - -patches = ['non-static.patch'] - -files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] - - -sanity_check_paths = { - 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', 'bin/guidedalign', 'bin/pbmask'], - 'dirs': [], -} - -makeopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' - -dependencies = [ - ('HDF5', '1.8.9'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..0db39afce4 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -0,0 +1,52 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'MakeCp' + +name = 'blasr' +version = 'smrtanalysis-2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + +patches = ['blasr-%(version)s_non-static.patch'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', + 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', + 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', + 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', + 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', + 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', + 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', + 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] + + +sanity_check_paths = { + 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', + 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', + 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', + 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', + 'bin/guidedalign', 'bin/pbmask'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/non-static.patch b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch similarity index 100% rename from easybuild/easyconfigs/b/blasr/non-static.patch rename to easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch -- GitLab From 623b9a8744d9f9809a3f49c8b86354921bb6dd4a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:56:59 +0200 Subject: [PATCH 0359/1172] get rid of shared_lib_ext --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index c793f86806..a53d8baacf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -28,7 +28,7 @@ osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], -- GitLab From 7c76bcac1439ec43ce6d2a4a6e65226c73651c6a Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:58:17 +0200 Subject: [PATCH 0360/1172] readded missing zlib-goolf-1.7.20 easyconfig --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 977 ++++++++++++++++++ 1 file changed, 977 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb new file mode 100644 index 0000000000..1b7ded7c48 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -0,0 +1,977 @@ + + + + + + + + + + + + easybuild-easyconfigs/zlib-1.2.8-goolf-1.7.20.eb at develop · hpcugent/easybuild-easyconfigs · GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
+ + + + + + + + + + +
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+ +
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+ + + + +

+ + /easybuild-easyconfigs + + + + + +

+
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+
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+

HTTPS clone URL

+
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Subversion checkout URL

+
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You can clone with +
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+ +
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+ + + branch: + develop + + + +
+ +
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+ +
+ easybuild-easyconfigs/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +
+
+ + +
+
+ @pescobar + pescobar + +
+ added zlib easyconfig for goolf-1.7.20 +
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+ 23 lines (16 sloc) + + 0.697 kB +
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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': 'goolf', 'version': '1.7.20'}
toolchainopts = {'optarch': True, 'pic': True}
+
source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')]
sources = [SOURCELOWER_TAR_GZ]
+
sanity_check_paths = {
'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'],
'dirs': [],
}
+
moduleclass = 'lib'
+ +
+ +
+ +Jump to Line + + +
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+ + + Something went wrong with that request. Please try again. +
+ + + + + + + + + -- GitLab From 5147003a015563b7a0cb65936a8641fe46aa4c88 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:58:27 +0200 Subject: [PATCH 0361/1172] properly fixed .eb name now --- .../t/tecplot360ex/tecplot360ex-linux64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb new file mode 100644 index 0000000000..08531bb3f3 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' -- GitLab From 2867e79d2362281a15c99490bff3cc4c68fd103d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 16:03:45 +0200 Subject: [PATCH 0362/1172] added right zlib easyconfig --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 987 +----------------- 1 file changed, 16 insertions(+), 971 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 1b7ded7c48..2e006a7aca 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -1,977 +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.""" - - - - - - - - - easybuild-easyconfigs/zlib-1.2.8-goolf-1.7.20.eb at develop · hpcugent/easybuild-easyconfigs · GitHub - - - - - - - +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} - - - - - - - - +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_GZ] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
- - - - - - - - - - -
-
-
- -
-
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- - - - -

- - /easybuild-easyconfigs - - - - - -

-
-
- -
-
-
- - - -
- -
-

HTTPS clone URL

-
- - - - -
-
- - -
-

Subversion checkout URL

-
- - - - -
-
- - - -
You can clone with -
or
. - - - -
- - - - - - - Download ZIP - -
-
- -
- - - - - - - -
- -
- - - branch: - develop - - - -
- -
- - - - -
- -
- easybuild-easyconfigs/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb -
-
- - -
-
- @pescobar - pescobar - -
- added zlib easyconfig for goolf-1.7.20 -
-
- -
-

- - 1 - contributor - -

- -
- -
- -
-
-
- -
- Raw - Blame - History -
- - - - - -
- -
- 23 lines (16 sloc) - - 0.697 kB -
-
- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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': 'goolf', 'version': '1.7.20'}
toolchainopts = {'optarch': True, 'pic': True}
-
source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')]
sources = [SOURCELOWER_TAR_GZ]
-
sanity_check_paths = {
'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'],
'dirs': [],
}
-
moduleclass = 'lib'
- -
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- -Jump to Line - - -
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- - - Something went wrong with that request. Please try again. -
- - - - - - - - +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} +moduleclass = 'lib' -- GitLab From c6f55c370d466780d4cc7055e3384478b32f7f15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:03:52 +0200 Subject: [PATCH 0363/1172] fix long line --- .../b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 0db39afce4..44a2388e5e 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -13,7 +13,9 @@ name = 'blasr' version = 'smrtanalysis-2.1' homepage = 'https://github.com/PacificBiosciences/blasr' -description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the + highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's + extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 5e8e28a8dd7a03eedc020708f7384c196422e25f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 16:16:33 +0200 Subject: [PATCH 0364/1172] removed old file --- .../t/tecplot360ex/tecplot-360ex.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb deleted file mode 100644 index 08531bb3f3..0000000000 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Binary' - -name = 'tecplot360ex' -version = 'linux64' - -homepage = 'http://www.tecplot.com/' -description = """ - Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, - and communicate your results with professional images and animations. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# fi. http://www.tecplot.com/my/product-releases/ -installername = '%(name)s_%(version)s.sh' -sources = [installername] - -sanity_check_paths = { - 'files': ['bin/tec360'], - 'dirs': [] -} -install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) - -moduleclass = 'vis' -- GitLab From e7194f07e4d1c4257263134c7ed677caaa36f807 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:44:23 +0200 Subject: [PATCH 0365/1172] fix style remarks --- .../blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 26 +++++++------------ 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 44a2388e5e..31e32665e9 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -17,7 +17,6 @@ description = """BLASR (Basic Local Alignment with Successive Refinement) rapidl highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" - toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,28 +25,21 @@ source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] patches = ['blasr-%(version)s_non-static.patch'] -dependencies = [ - ('HDF5', '1.8.9'), -] +dependencies = [('HDF5', '1.8.9')] buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' -files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', - 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', - 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', - 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', - 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', - 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', - 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', - 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] +binaries = [ + 'wordCounter', 'printReadWordCount', 'blasr', 'sdpMatcher', 'swMatcher', 'kbandMatcher', 'sawriter', + 'saquery', 'samodify', 'printTupleCountTable', 'malign', 'cmpPrintTupleCountTable', 'removeAdapters', + 'tabulateAlignment', 'samatcher', 'sals', 'saprinter', 'buildQualityValueProfile', 'extendAlign', + 'guidedalign', 'pbmask', +] +files_to_copy = [(['alignment/bin/%s' x for x in binaries], 'bin')] sanity_check_paths = { - 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', - 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', - 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', - 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', - 'bin/guidedalign', 'bin/pbmask'], + 'files': ['bin/%s' % x for x in binaries], 'dirs': [], } -- GitLab From 8300b3c48cb90f7c4ed4a56ae1cfab0d879aa41d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:52:20 +0200 Subject: [PATCH 0366/1172] fix typo --- .../easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 31e32665e9..d339980b4f 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -36,7 +36,7 @@ binaries = [ 'guidedalign', 'pbmask', ] -files_to_copy = [(['alignment/bin/%s' x for x in binaries], 'bin')] +files_to_copy = [(['alignment/bin/%s' % x for x in binaries], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % x for x in binaries], -- GitLab From 4231891afb0d0cfc6ee47eb7c2702bf3b14013f8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 16:54:31 +0200 Subject: [PATCH 0367/1172] changed url --- easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb index 08531bb3f3..40607b6960 100644 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -3,7 +3,7 @@ easyblock = 'Binary' name = 'tecplot360ex' version = 'linux64' -homepage = 'http://www.tecplot.com/' +homepage = 'http://www.tecplot.com/products/tecplot-360/' description = """ Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations. -- GitLab From 8b83f0ef72d0a2f1bfb77386455d25d56706b3ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:56:11 +0200 Subject: [PATCH 0368/1172] style fixes in PLUMED easyconfig --- .../PLUMED-2.0.4-ictce-7.1.2.eb} | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/p/{plumed/plumed-2.0.4-ictce-7.1.2.eb => PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb} (50%) diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb similarity index 50% rename from easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb index 3eda065ef1..aaa2734422 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -1,25 +1,22 @@ -# This is a quickly made easyconfig, using some dirty tricks... -# Warning: Here be dragons # by Ward Poelmans easyblock = 'ConfigureMake' -name = 'plumed' +name = 'PLUMED' version = '2.0.4' 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. + 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': 'ictce', 'version': '7.1.2'} -# Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url source_urls = ['https://github.com/plumed/plumed2/archive/'] -sources = ['v2.0.4.tar.gz'] +sources = ['v%(version)s.tar.gz'] patches = ['configure-%(version)s.patch'] @@ -31,7 +28,6 @@ sanity_check_paths = { 'dirs': ['lib/plumed'] } -# should probably happen in a easyblock. This vars needs to be set modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} moduleclass = 'chem' -- GitLab From ba3328abf9f4af33dc63bc71c8a472e4c3220a0b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 17:00:18 +0200 Subject: [PATCH 0369/1172] fixed remarks --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index cc5cb2cc40..8821d58210 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -11,6 +11,7 @@ version = '0.2.6' homepage = 'http://samtools.sourceforge.net' description = """ Generic indexer for TAB-delimited genome position files """ + toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] -- GitLab From a133fd1d6d12dc26202cf39ce7b8465b6f1ee3ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 17:10:16 +0200 Subject: [PATCH 0370/1172] move/rename patch for PLUMED --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb | 2 +- .../PLUMED-2.0.4_eb-env-vars.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/{plumed/configure-2.0.4.patch => PLUMED/PLUMED-2.0.4_eb-env-vars.patch} (100%) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb index aaa2734422..b6955fcdcc 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} source_urls = ['https://github.com/plumed/plumed2/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['configure-%(version)s.patch'] +patches = ['PLUMED-%(version)s_eb-env-vars.patch'] preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " diff --git a/easybuild/easyconfigs/p/plumed/configure-2.0.4.patch b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch similarity index 100% rename from easybuild/easyconfigs/p/plumed/configure-2.0.4.patch rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch -- GitLab From 44d2e4e1f678d3006e1ba5cc0aed04b9893094d6 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 18:16:05 +0200 Subject: [PATCH 0371/1172] fixed patch file --- .../easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch index 278b2edf59..6021cbe107 100644 --- a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -1,12 +1,12 @@ diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile ---- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 -+++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-03-14 23:21:04.221640935 +0100 +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 @@ -12,7 +12,7 @@ - PROG= samtools_0.1.18 - INCLUDES= -I. - SUBDIRS= . bcftools + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools -LIBPATH= +LIBPATH= -L$(EBROOTZLIB)/lib - LIBCURSES= -lcurses - + LIBCURSES= -lcurses + .SUFFIXES:.c .o -- GitLab From 2bb7142c64e9986632e75caff64e49854dd3da1d Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 18:26:52 +0200 Subject: [PATCH 0372/1172] fixed remarks --- ...apps.eb => ECore-1.5.2-ictce-5.5.0-clusterapps.eb} | 11 ++++++----- .../{ECore-1.5.2.eb => ECore-1.5.2-ictce-5.5.0.eb} | 7 ++++--- 2 files changed, 10 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/ECore/{ECore-1.5.2-clusterapps.eb => ECore-1.5.2-ictce-5.5.0-clusterapps.eb} (71%) rename easybuild/easyconfigs/e/ECore/{ECore-1.5.2.eb => ECore-1.5.2-ictce-5.5.0.eb} (76%) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb similarity index 71% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 6bfb37241d..4975ea635d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -5,20 +5,21 @@ version = '1.5.2' versionsuffix = '-clusterapps' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz')] patches = ['ecore-license-var.patch'] # needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 -dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', - 'orterun', 'packer', 'randomwalkffmpi', + 'orterun', 'packer', 'randomwalkffmpi', 'unpacker']] + \ ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb similarity index 76% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb index 5e6f6b0b1c..7c028041b8 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb @@ -4,15 +4,16 @@ name = 'ECore' version = '1.5.2' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From fb559c91cb226728656a55ae6fe057cd7340f69d Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 18:37:22 +0200 Subject: [PATCH 0373/1172] fixed typo --- .../easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 4975ea635d..ca072da66b 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -10,7 +10,7 @@ description = """The e-Core technology simulates the natural processes of sedime toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz')] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] patches = ['ecore-license-var.patch'] -- GitLab From 7bf7620290126a28b9f8fe49e169f5553339a52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 18:44:26 +0200 Subject: [PATCH 0374/1172] include missing libxml2 dep in GLib easyconfigs --- .../g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb | 1 + .../g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 1 + .../GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb | 1 + .../g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 1 + .../g/GLib/GLib-2.34.3-goolf-1.5.14.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-4.0.6.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-4.1.13.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-5.2.0.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-5.3.0.eb | 1 + .../g/GLib/GLib-2.40.0-goolf-1.5.14.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2014b.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2015a.eb | 2 ++ .../g/GLib/GLib-2.41.2-intel-2014b.eb | 1 + .../g/GLib/GLib-2.42.1-GCC-4.9.2.eb | 1 + .../g/GLib/GLib-2.42.1-foss-2015a.eb | 2 ++ .../l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb | 23 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb | 23 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb | 23 +++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.6.3.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.7.2.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.7.3.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.8-GCC-4.8.3.eb | 22 ++++++++++++++++++ 28 files changed, 285 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb index 0154f92cba..712b89daa3 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.8.1')), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index b3f747f733..73f392ace7 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.6.3')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb index 33fdefa087..2dfca0139b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.7.3')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index fe8be618bc..0b921d9d01 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.7.2')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb index 524a65b421..3abdd2956b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.8.2')), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb index 7330ea1391..1aa508846f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb index 66974822a8..81bd44a395 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb index 6e94d0afc6..f5ec30578d 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb index d913bace56..592b0e9587 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb index 70218fe010..ddf2f99faa 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.2')), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb index 0b2f10e82d..18e101a94a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb index be10bd30c3..73012be0a1 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb index 6732978735..ba5297e69e 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb @@ -15,6 +15,8 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index cec860f2de..cf844710e9 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb index 8db2b243a8..acba6c86f0 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index 167d8fc75b..aa417b69e0 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -15,6 +15,8 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb new file mode 100644 index 0000000000..f23eb301d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb @@ -0,0 +1,22 @@ +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': '4.6.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb new file mode 100644 index 0000000000..c70f20afe3 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..8a43c4c25e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb new file mode 100644 index 0000000000..c26849960b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.1'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..c19288a2fa --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..232c2e480f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb new file mode 100644 index 0000000000..4fc4a74955 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000..9291662776 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb new file mode 100644 index 0000000000..a6b6f7f14b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'GCC', 'version': '4.6.3'} +toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb new file mode 100644 index 0000000000..f2216d86e1 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'GCC', 'version': '4.7.2'} +toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb new file mode 100644 index 0000000000..572b633565 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'GCC', 'version': '4.7.3'} +toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb new file mode 100644 index 0000000000..1a28c0fbf0 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.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': 'GCC', 'version': '4.8.3'} +toolchainopts = {'optarch': True, '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 fba60a93b13e73b907a4b14174e10e260a3846ed Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 19:18:17 +0200 Subject: [PATCH 0375/1172] fixed remarks --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 808db8594a..4ab3c4b882 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -19,6 +19,8 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), @@ -27,7 +29,6 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 8821d58210..355e0eb0ad 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -19,6 +19,8 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), @@ -27,7 +29,6 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From dabb53e8595bb31e25365f5926bd8bfd8cb6b85d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 19:18:42 +0200 Subject: [PATCH 0376/1172] fixed small style remarks by @fgeorgatos --- easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index aaedf45292..486d2e128c 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -28,8 +28,7 @@ files_to_copy = [(["STAR"], "bin"), "README.txt"] sanity_check_paths = { 'files': ["bin/STAR"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' - -- GitLab From 589703db14101b2cfc569f6bcaf60da1f97e7109 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 19:23:03 +0200 Subject: [PATCH 0377/1172] style fixes --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index 76fe9f0898..a4cefde064 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -35,7 +35,7 @@ options = {'modulename': 'POSIX'} sanity_check_paths = { 'files': ["bin/scanms"], - 'dirs': [""] + 'dirs': [] } # copy all the documentation provided in the tarball to install directory -- GitLab From 024e73ba8320b97706e8b7c4521dd64d27068057 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:17:33 +0200 Subject: [PATCH 0378/1172] bump tophat version --- .../t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 36 +++++++++++++++++++ .../t/TopHat/tophat-2.0.14-zlib.patch | 12 +++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb new file mode 100644 index 0000000000..c12d3673ed --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.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 = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.14' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-%(version)s-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch new file mode 100644 index 0000000000..6021cbe107 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o -- GitLab From fc4a6d0e7227e2bda414fbcdb1450e336fa7e921 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:28:09 +0200 Subject: [PATCH 0379/1172] removed duplicated patch file --- .../t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 2 +- .../easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch | 12 ------------ 2 files changed, 1 insertion(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb index c12d3673ed..a2c8c49b14 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -17,7 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] -patches = ['tophat-%(version)s-zlib.patch'] +patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ ('Boost', '1.55.0'), diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch deleted file mode 100644 index 6021cbe107..0000000000 --- a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile ---- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 -+++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 -@@ -12,7 +12,7 @@ - PROG= samtools_0.1.18 - INCLUDES= -I. - SUBDIRS= . bcftools --LIBPATH= -+LIBPATH= -L$(EBROOTZLIB)/lib - LIBCURSES= -lcurses - - .SUFFIXES:.c .o -- GitLab From 361318413eff3b032094994d011c9b084e434d39 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:48:24 +0200 Subject: [PATCH 0380/1172] removed sanity check hack --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index a4cefde064..b40b1b8d7a 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -29,9 +29,8 @@ dependencies = [ (perl, perlver), ] -# workaround so sanity check in the PerlModule easyblock works. -# Just check the existence of a perl core module -options = {'modulename': 'POSIX'} +# override the default sanity check for perl packages which tries to load Perl module +exts_filter = ('scanms -v 2>&1 | grep version', "") sanity_check_paths = { 'files': ["bin/scanms"], -- GitLab From 83d0b63e4b843b26d9ec83e5a0ee23384fa17c12 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:00:25 +0200 Subject: [PATCH 0381/1172] switch from premakeopts to prebuildopts --- easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index 486d2e128c..c428723fec 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -20,7 +20,7 @@ sources = ['%(name)s_%(version)s.tgz'] patches = ['STAR_missing_includes.patch'] # a binary is provided with the source files. We delete it -premakeopts = 'rm STAR && ' +prebuildopts = 'rm STAR && ' parallel = 1 -- GitLab From f4979b40b64b15a803076bacd4b615022c889e52 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:06:15 +0200 Subject: [PATCH 0382/1172] style fixes in files_to_copy --- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index f573781fab..1ac74ecb09 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -24,9 +24,15 @@ dependencies = [('SAMtools', '0.1.19')] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -files_to_copy = [(['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), - "demo", "gmt", "gmt-web", "test", "README.md", "RELEASE" - ] +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] -- GitLab From 3e2900d865cbf1071920a0a5d686fcdc39854b55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:06:46 +0200 Subject: [PATCH 0383/1172] add missing easyblock spec --- easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb index 742fe0d215..d4e5cc4292 100644 --- a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'LAMARC' version = '2.1.9' versionsuffix = '-headless' -- GitLab From 0a7faf654af73591e753d7e399d87e442efa82cd Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:11:19 +0200 Subject: [PATCH 0384/1172] added missing zlib dependency --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 1ac74ecb09..3f76c20eb4 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -20,7 +20,10 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/genome/pindel/archive/'] sources = ['v%(version)s.tar.gz'] -dependencies = [('SAMtools', '0.1.19')] +dependencies = [ + ('SAMtools', '0.1.19'), + ('zlib', '1.2.8') +] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -- GitLab From 508c3e22b75d2aea284e3b97aa30ebbec3ab2f84 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:17:55 +0200 Subject: [PATCH 0385/1172] removed post install cmds, added patch --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch | 9 +++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 3f76c20eb4..41822a6052 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -20,6 +20,8 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/genome/pindel/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['pindel-perl-path.patch'] + dependencies = [ ('SAMtools', '0.1.19'), ('zlib', '1.2.8') @@ -37,8 +39,6 @@ files_to_copy = [ "RELEASE" ] -postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] - sanity_check_paths = { 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], 'dirs': [], diff --git a/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch new file mode 100644 index 0000000000..db0214c680 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch @@ -0,0 +1,9 @@ +diff -ru pindel-0.2.5a7.orig/bam2pindel.pl pindel-0.2.5a7/bam2pindel.pl +--- pindel-0.2.5a7.orig/bam2pindel.pl 2014-09-16 20:53:13.000000000 +0200 ++++ pindel-0.2.5a7/bam2pindel.pl 2015-06-03 21:12:57.775900885 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/env perl + + ######################################################################################################## + # # -- GitLab From 97eaf188766668743df86babdb1efdd452451f39 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:21:03 +0200 Subject: [PATCH 0386/1172] switched to prebuildopts --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 43d9e4ed11..92c332b06d 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -28,7 +28,7 @@ sources = ['idba-%(version)s.tar.gz'] premakeopts = './configure && ' # we delete every .o file which is left in bin folder -makeopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' +buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] @@ -39,4 +39,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 68bdbcd2d19a172064d419bb816ca938bda550a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:21:50 +0200 Subject: [PATCH 0387/1172] fix typo --- .../b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb index e24751cd72..5954f54393 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb @@ -10,7 +10,7 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] -sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.18.2' -- GitLab From ebc370953e34d38dd9020e14ec2152877671df27 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:24:26 +0200 Subject: [PATCH 0388/1172] switched to prebuildopts --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 92c332b06d..0ee4a4f740 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -25,7 +25,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://hku-idba.googlecode.com/files/'] sources = ['idba-%(version)s.tar.gz'] -premakeopts = './configure && ' +prebuildopts = './configure && ' # we delete every .o file which is left in bin folder buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' -- GitLab From 7aa4fbb40ec156297b18592fafa388ea5c809823 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:27:00 +0200 Subject: [PATCH 0389/1172] added missing easyblock line --- easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb index e63d0852ef..665f1371cb 100644 --- a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = "Check" version = "0.9.12" -- GitLab From 8bab0c90523ae32e3688a9e107425281f41b75da Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:28:47 +0200 Subject: [PATCH 0390/1172] fixed indentation --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index b40b1b8d7a..88fe827b03 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -33,8 +33,8 @@ dependencies = [ exts_filter = ('scanms -v 2>&1 | grep version', "") sanity_check_paths = { - 'files': ["bin/scanms"], - 'dirs': [] + 'files': ["bin/scanms"], + 'dirs': [] } # copy all the documentation provided in the tarball to install directory -- GitLab From 26d6ec222c34367c74c82a1c7cb28ea400eb67b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:29:25 +0200 Subject: [PATCH 0391/1172] fix LAMARC filename --- ...-2.1.9-ictce-5.5.0.eb => LAMARC-2.1.9-ictce-5.5.0-headless.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/LAMARC/{LAMARC-2.1.9-ictce-5.5.0.eb => LAMARC-2.1.9-ictce-5.5.0-headless.eb} (100%) diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb similarity index 100% rename from easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb rename to easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb -- GitLab From 5949aa6043031d72e35405904d82e2dac095b680 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:32:13 +0200 Subject: [PATCH 0392/1172] renamed as @boegel suggested --- ...k_Vina-1.1.2-linux_x86.eb => AutoDock_Vina-1.1.2_linux_x86.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/AutoDock_Vina/{AutoDock_Vina-1.1.2-linux_x86.eb => AutoDock_Vina-1.1.2_linux_x86.eb} (100%) diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb similarity index 100% rename from easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb rename to easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb -- GitLab From a30448b8157c934c9778570454a7670984cb1be1 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:35:16 +0200 Subject: [PATCH 0393/1172] switched to zlib-1.2.7 --- easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 41822a6052..65d0c45c59 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -24,7 +24,7 @@ patches = ['pindel-perl-path.patch'] dependencies = [ ('SAMtools', '0.1.19'), - ('zlib', '1.2.8') + ('zlib', '1.2.7') ] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -- GitLab From 73c49e1cc1bff2877cce7dd1b2d6d1ea34915357 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:43:15 +0200 Subject: [PATCH 0394/1172] added Boost-1.58.0-goolf-1.7.20.eb --- .../b/Boost/Boost-1.58.0-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8f65c8b894 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +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 91f2b1d488c0725723a731eb56ad51d5744f6a1d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:43:56 +0200 Subject: [PATCH 0395/1172] bump to latest boost in tophat easyconfig --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb index a2c8c49b14..6743572399 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -20,7 +20,7 @@ source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ - ('Boost', '1.55.0'), + ('Boost', '1.58.0'), ('zlib', '1.2.8'), ] -- GitLab From 8ae3cf405b4060a3d3d6d492798c6ea30fb755bc Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:48:55 +0200 Subject: [PATCH 0396/1172] renamed as @boegel suggested --- ...E2-2.3.0-x86_64_dynamic.eb => IMPUTE2-2.3.0_x86_64_dynamic.eb} | 0 ...UTE2-2.3.0-x86_64_static.eb => IMPUTE2-2.3.0_x86_64_static.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/IMPUTE2/{IMPUTE2-2.3.0-x86_64_dynamic.eb => IMPUTE2-2.3.0_x86_64_dynamic.eb} (100%) rename easybuild/easyconfigs/i/IMPUTE2/{IMPUTE2-2.3.0-x86_64_static.eb => IMPUTE2-2.3.0_x86_64_static.eb} (100%) diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb similarity index 100% rename from easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb rename to easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb similarity index 100% rename from easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb rename to easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb -- GitLab From 338788f1318b804748052fb9c6ec64ba2b644d7b Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:51:37 +0200 Subject: [PATCH 0397/1172] moved easyblock line to top --- .../c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb index 815406dfba..f772aaa29c 100644 --- a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -3,11 +3,11 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'MakeCp' + name = 'CONTRAfold' version = '2.02' -easyblock = 'MakeCp' - homepage = 'http://contra.stanford.edu/contrafold/' description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' @@ -21,7 +21,7 @@ patches = ['contrafold-gcc47.patch'] start_dir = 'src' files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/score_prediction', 'bin/contrafold'], -- GitLab From 4ed7c6cea54b2608edda2ed5878ae14922900a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 08:36:02 +0200 Subject: [PATCH 0398/1172] fix style issue --- easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb index 8f65c8b894..bee3eb38e4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -12,7 +12,8 @@ source_urls = [SOURCEFORGE_SOURCE] dependencies = [ ('bzip2', '1.0.6'), - ('zlib', '1.2.8')] + ('zlib', '1.2.8'), +] configopts = '--without-libraries=python' -- GitLab From ab02f47ebfbff434dc834e7217c01c759bac2911 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 11:08:00 +0200 Subject: [PATCH 0399/1172] {toolchain} GNU 5.1.0-2.25 --- .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 35 +++++++++++++ .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 52 +++++++++++++++++++ easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb | 20 +++++++ .../zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 23 ++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb 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 new file mode 100644 index 0000000000..fa4ce3cee9 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('zlib', '1.2.8'), + ('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 +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/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..b9370c56ff --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,52 @@ +name = "GCC" +version = '5.1.0' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': 'dummy'} + +mpfr_version = '3.1.2' + +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 = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.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/GNU/GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..684b3462cf --- /dev/null +++ b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'GNU' +gccver = '5.1.0' +binutilsver = '2.25' +version = '%s-%s' % (gccver, binutilsver) + +homepage = 'http://www.gnu.org/software/' +description = "Compiler-only toolchain with GCC and binutils." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # GCC built on top of (dummy-built) binutils + ('GCC', gccver, '-binutils-%s' % binutilsver), + # binutils built on top of GCC, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCC', '%s-binutils-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..d10f6ce0ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,23 @@ +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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 132a763aab0d19da7882a8c8f3c8f849f60b00f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 12:39:15 +0200 Subject: [PATCH 0400/1172] fix toolchain for libxml2 deps in GLib easyconfigs --- .../g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb | 2 +- .../g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 2 +- .../GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb | 2 +- .../g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 2 +- .../g/GLib/GLib-2.34.3-goolf-1.5.14.eb | 2 +- .../g/GLib/GLib-2.40.0-goolf-1.5.14.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2014b.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2015a.eb | 1 - .../g/GLib/GLib-2.41.2-intel-2014b.eb | 2 +- .../l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb | 22 ------------------- ...4.6.3.eb => libxml2-2.9.1-gmpolf-1.4.8.eb} | 2 +- ... => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} | 2 +- ...4.7.2.eb => libxml2-2.9.1-goolf-1.5.14.eb} | 2 +- ...4.8.3.eb => libxml2-2.9.2-goolf-1.5.14.eb} | 2 +- ....8.2.eb => libxml2-2.9.2-intel-2014.06.eb} | 6 ++--- ...-4.8.2.eb => libxml2-2.9.2-intel-2014b.eb} | 2 +- .../z/zlib/zlib-1.2.7-GCC-4.6.3.eb | 22 ------------------- .../z/zlib/zlib-1.2.7-GCC-4.7.2.eb | 22 ------------------- .../z/zlib/zlib-1.2.7-GCC-4.7.3.eb | 22 ------------------- .../z/zlib/zlib-1.2.8-GCC-4.8.3.eb | 22 ------------------- 21 files changed, 17 insertions(+), 128 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.6.3.eb => libxml2-2.9.1-gmpolf-1.4.8.eb} (90%) 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} (89%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.7.2.eb => libxml2-2.9.1-goolf-1.5.14.eb} (90%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.2-GCC-4.8.3.eb => libxml2-2.9.2-goolf-1.5.14.eb} (90%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.8.2.eb => libxml2-2.9.2-intel-2014.06.eb} (80%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.2-GCC-4.8.2.eb => libxml2-2.9.2-intel-2014b.eb} (90%) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb index 712b89daa3..d6ca2142ee 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.8.1')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index 73f392ace7..810a19f768 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.6.3')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb index 2dfca0139b..c01d10d566 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.7.3')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index 0b921d9d01..767bcb84db 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.7.2')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb index 3abdd2956b..4ce11348bb 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.8.2')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb index ddf2f99faa..a72a4d209a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.2')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb index 18e101a94a..f22199ae2b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb index 73012be0a1..feabab52c2 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb index ba5297e69e..f5b201076b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb @@ -16,7 +16,6 @@ dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index cf844710e9..207b74b508 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -14,7 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb deleted file mode 100644 index c26849960b..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb +++ /dev/null @@ -1,22 +0,0 @@ -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': '4.8.1'} - -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', '1.2.7')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index f23eb301d6..4f35163694 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -7,7 +7,7 @@ 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': '4.6.3'} +toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ 'http://xmlsoft.org/sources/', 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 89% 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 8a43c4c25e..6e4ab86218 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 @@ -7,7 +7,7 @@ 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/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index c70f20afe3..42fd9996e9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -7,7 +7,7 @@ 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': '4.7.2'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ 'http://xmlsoft.org/sources/', 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-goolf-1.5.14.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index 9291662776..e2bb547666 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -8,7 +8,7 @@ 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'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb similarity index 80% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index c19288a2fa..aae9d0148e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' name = 'libxml2' -version = '2.9.1' +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': '4.8.2'} +toolchain = {'name': 'intel', 'version': '2014.06'} source_urls = [ 'http://xmlsoft.org/sources/', @@ -18,6 +18,6 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 4fc4a74955..52ee0616b0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -8,7 +8,7 @@ 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': '4.8.2'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb deleted file mode 100644 index a6b6f7f14b..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -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': 'GCC', 'version': '4.6.3'} -toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb deleted file mode 100644 index f2216d86e1..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -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': 'GCC', 'version': '4.7.2'} -toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb deleted file mode 100644 index 572b633565..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -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': 'GCC', 'version': '4.7.3'} -toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb deleted file mode 100644 index 1a28c0fbf0..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -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': 'GCC', 'version': '4.8.3'} -toolchainopts = {'optarch': True, '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 783e26182242e9460fc377a6cd283a6c4f1b8424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 12:51:04 +0200 Subject: [PATCH 0401/1172] fix toolchain for libxml2 dep in GLib intel/2015a easyconfig --- easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index aa417b69e0..7f0fde608b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -16,7 +16,7 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] -- GitLab From 321625a11a897eecf2e9f62132af536b76fb8d06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 13:01:31 +0200 Subject: [PATCH 0402/1172] use older libxml2 version in GLib easyconfigs using old toolchain (for compatibility with existing DOLFIN easyconfigs) --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index 810a19f768..db0b390028 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index 767bcb84db..faced55c2c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb index 1aa508846f..3b25385b1f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] -- GitLab From 6dab59bc0d473da361da1a6c61a060a67d1bc3a6 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Thu, 4 Jun 2015 13:35:37 +0200 Subject: [PATCH 0403/1172] - SOBAcl-r18-intel-2014b-Perl-5.20.0.eb : added EasyConfig for SOBAcl --- .../SOBAcl-r18-intel-2014b-Perl-5.20.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..e58e9e902a --- /dev/null +++ b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,22 @@ +easyblock = "Tarball" + +name = 'SOBAcl' +version = 'r18' + +homepage = 'http://www.sequenceontology.org/software/sobacl.html' +description = """SOBAcl is a command line tool for analyzing GFF3 annotations. +GFF3 is a standard file format for genomic annotation data. SOBAcl gathers +statistics from GFF3 files and can generate a wide variety of tables +and graphs.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +sources = [('SOBA_%s.tar.gz' % (version))] +source_urls = ['http://www.sequenceontology.org/software/SOBA_Code/'] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [('GraphViz', '2.18', versionsuffix)] + +moduleclass = 'bio' -- GitLab From 784b9e81f1b93f257288eacc06378402e162e60f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 13:36:42 +0200 Subject: [PATCH 0404/1172] fix double dep --- easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index 7f0fde608b..8cf2990d69 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -16,7 +16,6 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] -- GitLab From 96abaf33719fac2b1fdb38a6a8fca7597562eb73 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Thu, 4 Jun 2015 13:48:59 +0200 Subject: [PATCH 0405/1172] - moved file --- .../GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{Graphviz => }/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) diff --git a/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb -- GitLab From bd80a031d510a0c2343980e760473a1271ee4dd0 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Thu, 4 Jun 2015 15:12:49 +0200 Subject: [PATCH 0406/1172] - changed source_urls and homepage --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb | 7 +++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb | 6 +++--- 13 files changed, 41 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index feb10d4a75..b6405c19b6 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index e8472dac11..54ce3a5791 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index c489c5aa68..7ff79c377b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 4a7a10534b..327564fbd3 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -1,15 +1,15 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index a411477c0b..1bfd983e7e 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 3c0ae0a9af..3644b946c0 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 7569a7cd7b..6abe0d811d 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index d39e90c9e4..7bcfcdfee8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -1,12 +1,15 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +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'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb index 312d6b1990..bfd0e1cd2f 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb index 2111ce217a..0bfab5d015 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [ - 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/', - 'http://master.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb index 6435694c00..a829af981d 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935..61b425c25a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index aa253ef5eb..7ca9946d90 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] -- GitLab From c5305829749516f37ebc83fbfebed7c0a519c298 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 19:00:46 +0200 Subject: [PATCH 0407/1172] include comment in patch file --- .../easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch index eef94268d9..ba79adb02e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -1,3 +1,5 @@ +replace svnversion call with mimiced output for non-SVN tarballs for older versions of svnversion, i.e 'exported' +author: Kenneth Hoste (Ghent University) --- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 +++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 @@ -4242,7 +4242,8 @@ -- GitLab From 04720cdff35327efe1f76b18add69f54fcafb678 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 20:24:47 +0200 Subject: [PATCH 0408/1172] fix patches redefinition in Python 2.5.6 ictce/4.x easyconfigs --- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 7 ++++--- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 5cad1244b7..23ddabe854 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,9 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index eecf1e2276..f747214b5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,9 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), -- GitLab From 04f0dfd8c6c008bfe0662dc4405cdc3ac656b167 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Fri, 5 Jun 2015 00:23:06 +0200 Subject: [PATCH 0409/1172] - fixed typo in source_urls for SQL::Abstract --- easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index afa1c420a1..c7d3a27ade 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -838,7 +838,7 @@ exts_list = [ }), ('SQL::Abstract', '1.81', { 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/S/'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], }), ('GD::Graph', '1.49', { 'source_tmpl': 'GDGraph-1.49.tar.gz', -- GitLab From 533e2e962832fc58cc5dc5bfa6ca5f59111d66f6 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 10:18:45 +0200 Subject: [PATCH 0410/1172] .eb file to install GenotypeHarmonizer version 1.4.14 with Java 1.7.0 --- ...GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb new file mode 100644 index 0000000000..153a9953dd --- /dev/null +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ + +name = 'GenotypeHarmonizer' +version = '1.4.14' + +homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' +description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +easyblock = 'PackedBinary' + +dependencies = [('Java', '1.7.0_80')] + +# +# Example URL +# http://www.molgenis.org/downloads/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-dist.tar.gz +# +download_name = 'Genotype-Harmonizer' +source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] +sources = ['GenotypeHarmonizer-%s-dist.tar.gz' % version] + +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] #GenotypeHarmonizer-1.4.14-dist.tar.gz + +sanity_check_paths = { + 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 086221427b3d2b1237def12ec15e26a673945a97 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 10:31:49 +0200 Subject: [PATCH 0411/1172] .eb file to install hisat 0.1.5 (beta) with goolf 1.7.20 --- .../h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb new file mode 100644 index 0000000000..ea115e16fb --- /dev/null +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -0,0 +1,33 @@ + +name = 'hisat' +version = '0.1.5-beta' + +homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' +description = """ +HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, +HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic +region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) +combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. +The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +easyblock = 'MakeCp' +# +# Example URL: +# http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.6-beta-source.zip +# +sources = ['%(name)s-%(version)s-source.zip'] +source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] + +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] # hisat-0.1.5-beta-source.zip + +executables = [name,'hisat-build','hisat-inspect','hisat-build-s','hisat-inspect-s','hisat-align-s','hisat-build-l','hisat-inspect-l','hisat-align-l'] +files_to_copy = [(executables, 'bin')] + + +sanity_check_paths = { + 'files': ['bin/%s' % name], + 'dirs': []} + +moduleclass = 'bio' -- GitLab From ff1a0123332cbaf59aebd7971891c749a9765a5b Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:12:31 +0200 Subject: [PATCH 0412/1172] Change formatting, remove unused variable, remove some coments --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 153a9953dd..73d9434519 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,3 +1,5 @@ +toolchain = {'name': 'dummy', 'version': 'dummy'} +easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' version = '1.4.14' @@ -5,20 +7,12 @@ version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} -easyblock = 'PackedBinary' - dependencies = [('Java', '1.7.0_80')] -# -# Example URL -# http://www.molgenis.org/downloads/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-dist.tar.gz -# -download_name = 'Genotype-Harmonizer' source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] -sources = ['GenotypeHarmonizer-%s-dist.tar.gz' % version] +sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] #GenotypeHarmonizer-1.4.14-dist.tar.gz +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] sanity_check_paths = { 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], -- GitLab From 63bd74aac9f22eb3fb7a3e152394651ccdbba66d Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:16:26 +0200 Subject: [PATCH 0413/1172] Add Java suffix --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 73d9434519..6df1f25684 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -7,7 +7,10 @@ version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -dependencies = [('Java', '1.7.0_80')] +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 6aa287531834b83ed81614bc5e6a09ad1b4b9ca3 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:22:56 +0200 Subject: [PATCH 0414/1172] Change structure, remove unnecesarry comments, make lines max 120 char long --- .../h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 32 +++++++++---------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb index ea115e16fb..259f21eb5b 100644 --- a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -1,33 +1,31 @@ +toolchain = {'name': 'goolf', 'version': '1.7.20'} +easyblock = 'MakeCp' name = 'hisat' version = '0.1.5-beta' homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' -description = """ -HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, -HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic -region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) -combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. -The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ +description = """HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one + global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover + the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the + human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective + alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively + low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the + operations on the FM index. """ -toolchain = {'name': 'goolf', 'version': '1.7.20'} - -easyblock = 'MakeCp' -# -# Example URL: -# http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.6-beta-source.zip -# sources = ['%(name)s-%(version)s-source.zip'] source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] -checksums = ['9524a0170d85c5b560b51e0087f4cf46'] # hisat-0.1.5-beta-source.zip +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] -executables = [name,'hisat-build','hisat-inspect','hisat-build-s','hisat-inspect-s','hisat-align-s','hisat-build-l','hisat-inspect-l','hisat-align-l'] +executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', + 'hisat-build-l', 'hisat-inspect-l', 'hisat-align-l'] files_to_copy = [(executables, 'bin')] sanity_check_paths = { - 'files': ['bin/%s' % name], - 'dirs': []} + 'files': ['bin/%(name)s'], + 'dirs': [], +} moduleclass = 'bio' -- GitLab From cd8f2801e79a9efdb70b598679db62701096d0fa Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:43:03 +0200 Subject: [PATCH 0415/1172] .eb file to install veryifyBamID-1.1.2 with goolf 1.7.20 --- .../verifyBamID-1.1.2-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..a567543a99 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +toolchain = {'name': 'goolf', 'version': '1.7.20'} +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.2' + +homepage = "http://csg.sph.umich.edu/kang/verifyBamID/index.html" +description = """verifyBamID is a software that verifies whether the reads in particular file match previously known + genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of + two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When + external genotypes are not available, verifyBamID still robustly detects sample swaps. +""" + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['fafc6fa58ba2bd51d0324ae616f5b29e'] + +buildopts = 'CXX="$CXX"' + +executables = ['%(name)s/bin/%(name)s'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'] +} + + +moduleclass = 'bio' -- GitLab From 419ef5a2e4ea30284b8dff41e15d7a2aaf1c58c3 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:47:13 +0200 Subject: [PATCH 0416/1172] move toolchain to correct position --- .../v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb index a567543a99..df27e86592 100644 --- a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'goolf', 'version': '1.7.20'} easyblock = 'MakeCp' name = 'verifyBamID' @@ -11,6 +10,8 @@ description = """verifyBamID is a software that verifies whether the reads in pa external genotypes are not available, verifyBamID still robustly detects sample swaps. """ +toolchain = {'name': 'goolf', 'version': '1.7.20'} + source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] sources = ['%(name)sLibStatGen.%(version)s.tgz'] -- GitLab From dfc74d982c4b96b0b3ab4b636978b892b7600ea6 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:50:20 +0200 Subject: [PATCH 0417/1172] move toolchain to correct position of GenotypeHarmonizer --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 6df1f25684..ae8a4779c4 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'dummy', 'version': 'dummy'} easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' @@ -12,6 +11,8 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] +toolchain = {'name': 'dummy', 'version': 'dummy'} + source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 04b6ed4336535e25724ba08e19a519be1ecfb236 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 14:59:26 +0200 Subject: [PATCH 0418/1172] Update GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 6df1f25684..e326971151 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -5,7 +5,8 @@ name = 'GenotypeHarmonizer' version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' -description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" +description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data + stored using different file formats with different and potentially unknown strands.""" java = 'Java' javaver = '1.7.0_80' -- GitLab From 3ee04bc72791a0240774684f74213bf48aac8996 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 15:12:35 +0200 Subject: [PATCH 0419/1172] .eb file to install STAR-2.3.1z12 with goolf-1.7.20 --- .../s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb new file mode 100644 index 0000000000..b2877e3d85 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.1z12' + +homepage = 'https://code.google.com/p/rna-star/' +description = """STAR: ultrafast universal RNA-seq aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/alexdobin/%(name)s/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] + +buildopts = 'CXX="$CXX"' + +executables = [name, 'STARstatic'] +files_to_copy = [(executables,'bin/')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' -- GitLab From 334012321056fd5f5009c1dd123aae2e267d7a9c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Jun 2015 15:28:57 +0200 Subject: [PATCH 0420/1172] 1st --- easybuild/easyconfigs/m/MCR/MCR-R2014a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2014a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb new file mode 100644 index 0000000000..7efec1287d --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -0,0 +1,16 @@ +name = 'MCR' +version = 'R2014a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies =[('Java', '1.8.0_31')] + +moduleclass = 'math' -- GitLab From 036e4afe8fedd7841aa803b15f2de4e98e7178dc Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:56:50 +0200 Subject: [PATCH 0421/1172] Update GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index e326971151..0fa0ab2a82 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'dummy', 'version': 'dummy'} easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' @@ -8,6 +7,8 @@ homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -- GitLab From 8cd4a7666d4d2e04af1b4bd8aa588116395b1d67 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:58:15 +0200 Subject: [PATCH 0422/1172] Update hisat-0.1.5-beta-goolf-1.7.20.eb toolchain under description --- easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb index 259f21eb5b..bd8c70bf67 100644 --- a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'goolf', 'version': '1.7.20'} easyblock = 'MakeCp' name = 'hisat' @@ -13,6 +12,8 @@ description = """HISAT is a fast and sensitive spliced alignment program for map low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ +toolchain = {'name': 'goolf', 'version': '1.7.20'} + sources = ['%(name)s-%(version)s-source.zip'] source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] -- GitLab From 975d6dea145980a328419ef84003a32f08b31a1b Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:59:52 +0200 Subject: [PATCH 0423/1172] Empty dirs list, removed double whiteline --- .../v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb index df27e86592..1d1bbb0d8a 100644 --- a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -24,8 +24,7 @@ files_to_copy = [(executables, 'bin')] sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': ['bin'] + 'dirs': [] } - moduleclass = 'bio' -- GitLab From 5d83a5b480707abec4cb12456e9274751d46dd6f Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 16:01:35 +0200 Subject: [PATCH 0424/1172] Empty dirs list --- easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb index b2877e3d85..2a0cc25f41 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -20,7 +20,7 @@ files_to_copy = [(executables,'bin/')] sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': ['bin'] + 'dirs': [] } moduleclass = 'bio' -- GitLab From ac88a9ae60798533125e3ff733a09e7fbc2117d6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 16:02:16 +0200 Subject: [PATCH 0425/1172] Extra space after executables, removed trailing / --- easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb index 2a0cc25f41..01b05100cc 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -16,7 +16,7 @@ checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] buildopts = 'CXX="$CXX"' executables = [name, 'STARstatic'] -files_to_copy = [(executables,'bin/')] +files_to_copy = [(executables, 'bin')] sanity_check_paths = { 'files': ['bin/%(name)s'], -- GitLab From 7ca80e3e4e7baded83582ec2cf48ae1a0d5e4fe3 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 5 Jun 2015 16:25:00 +0200 Subject: [PATCH 0426/1172] Adding the infiniband patch for OpenMPI --- .../openmpi-mca-params.conf-1.8.5-local.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch new file mode 100644 index 0000000000..f9fa71615a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch @@ -0,0 +1,12 @@ +--- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 ++++ opal/etc/openmpi-mca-params.conf 2015-06-05 16:21:05.855302000 +0200 +@@ -56,3 +56,9 @@ + + # See "ompi_info --param all all" for a full listing of Open MPI MCA + # parameters available and their default values. ++ ++# FG, 20130317; customization for University of Luxembourg systems ++btl_openib_if_exclude=mlx4_1 ++btl_openib_warn_nonexistent_if=0 ++orte_rsh_agent=oarsh ++btl_openib_memalign_threshold=12288 -- GitLab From d48b8df51270d1475929665777186e33948b514b Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Mon, 8 Jun 2015 10:37:40 +0200 Subject: [PATCH 0427/1172] Updating patch file --- .../o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch index f9fa71615a..0d7989a781 100644 --- a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch +++ b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch @@ -1,12 +1,9 @@ --- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 -+++ opal/etc/openmpi-mca-params.conf 2015-06-05 16:21:05.855302000 +0200 -@@ -56,3 +56,9 @@ ++++ opal/etc/openmpi-mca-params.conf 2015-06-08 10:36:05.387902000 +0200 +@@ -56,3 +56,6 @@ # See "ompi_info --param all all" for a full listing of Open MPI MCA # parameters available and their default values. + -+# FG, 20130317; customization for University of Luxembourg systems -+btl_openib_if_exclude=mlx4_1 -+btl_openib_warn_nonexistent_if=0 -+orte_rsh_agent=oarsh ++# Fix bug in the initialization of the value when using the infiniband module. (ref: http://www.open-mpi.org/community/lists/users/2015/05/26913.php) +btl_openib_memalign_threshold=12288 -- GitLab From 060dbaee4587aee036ed1edb18ce4336f0564715 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Mon, 8 Jun 2015 10:58:17 +0200 Subject: [PATCH 0428/1172] Adding patch to the easyconfigs --- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 5 ++++- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 5 ++++- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 5 ++++- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ++++ .../OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 5 +++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 4 ++++ .../OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 4 ++++ ...5-local.patch => openmpi-mca-params.conf-pre-1.8.6.patch} | 0 27 files changed, 103 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{openmpi-mca-params.conf-1.8.5-local.patch => openmpi-mca-params.conf-pre-1.8.6.patch} (100%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7..8037292116 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721..4439183191 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55..286b13e558 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945..84ed520e49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,6 +19,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_f77" ,"mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0..3f37ffe201 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7..5c8698cf2a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,6 +24,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e3449..0d4e8e1a10 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda8..c52fa56a7c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617..0adf96e75a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d..251f47e42c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfa..ccd7bda9e9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613df..cf9baf6195 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f..faf4a7a6d8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271..046590fd3c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,6 +18,10 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d..bb279bfe90 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b..d7b0f1bcd1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,6 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index fdf4f47fc8..2dd1f2e385 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -11,9 +11,10 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-%(version)s_common-cuda-lib.patch', - 'OpenMPI-%(version)s-vt_cupti_events.patch' + 'OpenMPI-%(version)s-vt_cupti_events.patch', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720..881ad83275 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd41..063c84b4a4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2..2bf0d5beb0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,6 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c..f4723656da 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -22,6 +22,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2..df7fe4109e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3b..6e2e0d1429 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f..d8a312b1ae 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,6 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6..2e31a0bff5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,6 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 17455567fb..275ab25d92 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + 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 ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch rename to easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch -- GitLab From 00fd39553d0fe8a0bdc8b3e882883ef486c490a6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 8 Jun 2015 11:11:29 +0200 Subject: [PATCH 0429/1172] Removed duplicated toolchain line --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 47397c2963..0fa0ab2a82 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -14,8 +14,6 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -toolchain = {'name': 'dummy', 'version': 'dummy'} - source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 367008cd44fb4095ca264b9ed912d50525186d94 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 8 Jun 2015 12:28:24 +0200 Subject: [PATCH 0430/1172] Adjusted Qt homepage and download URL --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb index e0d6a9d420..f353838078 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] -- GitLab From 106f2e27f32ef0a8747644868154e4d0090c7540 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:08:13 +0200 Subject: [PATCH 0431/1172] Add .eb files for snpEff v3.6 and snpEff v4.1d --- .../s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 31 +++++++++++++++++++ .../s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..6278b4ba19 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb @@ -0,0 +1,31 @@ +import time + +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +seconds_after_epoch = int(time.time()) +source_urls = [('http://downloads.sourceforge.net/project/%s?ts=%s&use_mirror=autoselect' % (name.lower(), seconds_after_epoch))] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000..7763b7baad --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb @@ -0,0 +1,31 @@ +import time + +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +seconds_after_epoch = int(time.time()) +source_urls = ['http://downloads.sourceforge.net/project/%(name.lower())s?ts=%(seconds_after_epoch)s&use_mirror=autoselect'] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 485b56534fa1575183454ec91041b388ca61650b Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:30:09 +0200 Subject: [PATCH 0432/1172] .eb file for SAMtools 0.1.19 with goolf 1.7.20 --- .../SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb new file mode 100644 index 0000000000..ceb5083895 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -0,0 +1,23 @@ + +name = 'SAMtools' +version = '0.1.19' + +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': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +checksums = ['ff8b46e6096cfb452003b1ec5091d86a'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 7cb1ac217609a76bfcd6121e84e1ad10eef6ca3e Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:42:50 +0200 Subject: [PATCH 0433/1172] .eb file for PLINK-1.07-x86_64-goolf-1.7.20 --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb new file mode 100644 index 0000000000..aa31391d7e --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = "plink-1.07-src: Whole-genome association analysis toolset" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + "plink", + "gPLINK.jar", + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["plink", "gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0c3e759c7413dfee31b4dcb1e8f30cac7719b82b Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:45:45 +0200 Subject: [PATCH 0434/1172] changed double quotes to single quotes to conform with other .eb files --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb index aa31391d7e..50bb76fbb3 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'PLINK' version = '1.07-x86_64' homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' -description = "plink-1.07-src: Whole-genome association analysis toolset" +description = 'plink-1.07-src: Whole-genome association analysis toolset' toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -14,16 +14,16 @@ source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] checksums = ['fd0bafeda42151b20534e4f97b0d97df'] files_to_copy = [ - "plink", - "gPLINK.jar", - "test.map", - "test.ped", - "COPYING.txt", - "README.txt", + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', ] sanity_check_paths = { - 'files': ["plink", "gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], 'dirs': [], } -- GitLab From 83ebc81820da3cba5d24fff87a4bcbc8398ec073 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 14:59:23 +0200 Subject: [PATCH 0435/1172] Change name of .eb file because it is already compiled (so goolf not used) --- .../easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb new file mode 100644 index 0000000000..50bb76fbb3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = 'plink-1.07-src: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f15b0f5792fba76b9644b0f36fe899ffc1538017 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 8 Jun 2015 15:12:44 +0200 Subject: [PATCH 0436/1172] Delete PLINK-1.07-x86_64-goolf-1.7.20.eb --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb deleted file mode 100644 index 50bb76fbb3..0000000000 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'PLINK' -version = '1.07-x86_64' - -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' -description = 'plink-1.07-src: Whole-genome association analysis toolset' - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['%(namelower)s-%(version)s.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] - -checksums = ['fd0bafeda42151b20534e4f97b0d97df'] - -files_to_copy = [ - 'plink', - 'gPLINK.jar', - 'test.map', - 'test.ped', - 'COPYING.txt', - 'README.txt', -] - -sanity_check_paths = { - 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From 918acfe57a9bc8d53cf9e38eb0df549dbc632336 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 3 Jun 2015 13:15:57 +0200 Subject: [PATCH 0437/1172] Add support for R pbd. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 +++++++++++++++++++ ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb create mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb new file mode 100644 index 0000000000..05e79faaa5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'R-bundle' +version = '20150605' +bundlename = 'pbd' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000..ae54615b78 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + -- GitLab From 56c5d760efd84b2fd311b99289b3f154caf0a638 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 15:04:48 +0200 Subject: [PATCH 0438/1172] Updated PDT easyconfigs - removed config parameter hackery now taken care of by custom easyblock - add checksums --- .../p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb | 36 +++++-------------- .../easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb | 36 +++++-------------- .../easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 35 +++++------------- 3 files changed, 27 insertions(+), 80 deletions(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb index a6ab7c4155..eef9a27cd7 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb index 7faa216ef2..f50e7519a2 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'ictce', 'version': '5.3.0'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index 124698a037..4acb86b021 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.20" @@ -23,27 +25,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -skipsteps = ['build'] - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + 'c3edabe202926abe04552e33cd39672d', # pdtoolkit-3.20.tar.gz +] moduleclass = 'perf' -- GitLab From 7943c8d70acbe73e7c67da54dcc235e25625ae57 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:03:35 +0200 Subject: [PATCH 0439/1172] Update to latest Vampir release, adding suggested parameters for silent installation --- ...x-x86_64.eb => Vampir-8.4.1-foss-2015a.eb} | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.1.0-linux-x86_64.eb => Vampir-8.4.1-foss-2015a.eb} (54%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb similarity index 54% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 7b467d1272..51ba49a2a0 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -1,16 +1,17 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## easyblock='Binary' name = "Vampir" -version = "8.1.0" -versionsuffix = "-linux-x86_64" +version = "8.4.1" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -18,15 +19,22 @@ description = """The VAMPIR software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%(version)s-standard%(versionsuffix)s-setup.bin'] +sources = ['vampir-%s-linux-x86_64-setup.bin' % (version)] -install_cmd = "./vampir-%(version)s-standard%(versionsuffix)s-setup.bin --silent --instdir=%(installdir)s" +install_cmd = "./vampir-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], 'dirs': [] } +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + moduleclass = 'perf' -- GitLab From 8a2ca653eef8ef14c4b8e78af2ed75ca255b6bd6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:04:57 +0200 Subject: [PATCH 0440/1172] Add corresponding easyconfig for VampirServer --- .../VampirServer-8.4.1-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb new file mode 100644 index 0000000000..2c7fb3e4eb --- /dev/null +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock='Binary' + +name = "VampirServer" +version = "8.4.1" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ['vampirserver-%s-linux-x86_64-setup.bin' % (version)] + +install_cmd = "./vampirserver-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" + +sanity_check_paths = { + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], + 'dirs': [] +} + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' -- GitLab From 654d988b7ce03021f8964724e2a0c660f1899c4d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:09:54 +0200 Subject: [PATCH 0441/1172] Use %(version)s where necessary --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 4 ++-- .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 51ba49a2a0..672d33cf47 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -21,9 +21,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%s-linux-x86_64-setup.bin' % (version)] +sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampir-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./vampir-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 2c7fb3e4eb..eb02b99c8b 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -22,9 +22,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -sources = ['vampirserver-%s-linux-x86_64-setup.bin' % (version)] +sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampirserver-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./vampirserver-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], -- GitLab From b277923e88621566d616ed3dd0a5f219a7d32bf7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 19:54:10 +0200 Subject: [PATCH 0442/1172] Apply change to install_cmd as requested by review --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 3 ++- .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 672d33cf47..0c1ff46f1b 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -8,6 +8,7 @@ # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock='Binary' name = "Vampir" @@ -23,7 +24,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampir-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index eb02b99c8b..f55fa79b0b 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -8,6 +8,7 @@ # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock='Binary' name = "VampirServer" @@ -24,7 +25,7 @@ toolchainopts = {"usempi": True} sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampirserver-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], -- GitLab From b63db539c28c29ab02c28b7e43f445c4555ab043 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 20:00:53 +0200 Subject: [PATCH 0443/1172] Add checksums --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 4 ++++ .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 0c1ff46f1b..5328137af1 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -24,6 +24,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] +checksums = [ + '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin +] + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index f55fa79b0b..4b737a9b8d 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -25,6 +25,10 @@ toolchainopts = {"usempi": True} sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] +checksums = [ + '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin +] + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { -- GitLab From 9c9bc2d63429032d4af4cf9be996c28ea9d27465 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:29:01 +0200 Subject: [PATCH 0444/1172] Added myself as an author --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 1 + .../easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 5328137af1..2b1dcd0556 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Markus Geimer # License:: 3-clause BSD # # This work is based on experiences from the UNITE project diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 4b737a9b8d..3710da1f32 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Markus Geimer # License:: 3-clause BSD # # This work is based on experiences from the UNITE project -- GitLab From 172f958d843229eb901ab5dac0b48cfd6bc0e86e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:30:59 +0200 Subject: [PATCH 0445/1172] Renamed files to reflect supported platform --- ....4.1-foss-2015a.eb => Vampir-8.4.1-linux-x86_64-foss-2015a.eb} | 0 ...oss-2015a.eb => VampirServer-8.4.1-linux-x86_64-foss-2015a.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1-linux-x86_64-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-foss-2015a.eb => VampirServer-8.4.1-linux-x86_64-foss-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb -- GitLab From bb8bba996ec6cd549de236a7e686624198f51de3 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:44:02 +0200 Subject: [PATCH 0446/1172] Make variant easily configurable --- .../v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb | 3 ++- .../VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb index 2b1dcd0556..b4541a5784 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb @@ -14,6 +14,7 @@ easyblock='Binary' name = "Vampir" version = "8.4.1" +variant = "linux-x86_64" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -23,7 +24,7 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] +sources = ['vampir-%s-%s-setup.bin' % (version, variant)] checksums = [ '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb index 3710da1f32..472f9c6a46 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb @@ -14,6 +14,7 @@ easyblock='Binary' name = "VampirServer" version = "8.4.1" +variant = "linux-x86_64" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -24,7 +25,7 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] +sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] checksums = [ '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin -- GitLab From fe5b11b6e66289c17d4c7c01bf679d5879e2c740 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:59:50 +0200 Subject: [PATCH 0447/1172] Add easyconfig for Vampir demo version --- ...mpir-8.4.1-demo-linux-x86_64-foss-2015a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb new file mode 100644 index 0000000000..f6afd9c0a1 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb @@ -0,0 +1,48 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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='Binary' + +name = "Vampir" +version = "8.4.1" +versionsuffix = "-demo" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] + +checksums = [ + '09cf28650be36516613372c8a0d1c0d8', # vampir-8.4.1-demo-linux-x86_64-setup.bin +] + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' -- GitLab From 46fc4a3221648c5eb50726c2345b561374ebf41f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 10:35:26 +0200 Subject: [PATCH 0448/1172] Modify the example license_file value as suggested --- .../v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb | 2 +- .../v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb | 2 +- .../VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb index f6afd9c0a1..42c77ab311 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb @@ -39,7 +39,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb index b4541a5784..ffb4fc26ad 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb @@ -38,7 +38,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb index 472f9c6a46..83d53b0104 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb @@ -39,7 +39,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, -- GitLab From 6f94a296a50a8952763305db3f376d6aad24f0a9 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 10:36:53 +0200 Subject: [PATCH 0449/1172] Remove variant from file name due to EB policy/limitation --- ...linux-x86_64-foss-2015a.eb => Vampir-8.4.1-demo-foss-2015a.eb} | 0 ....4.1-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-foss-2015a.eb} | 0 ...inux-x86_64-foss-2015a.eb => VampirServer-8.4.1-foss-2015a.eb} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-demo-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-linux-x86_64-foss-2015a.eb => VampirServer-8.4.1-foss-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb -- GitLab From ab60fa01e32da8f2bb3dbe45e7db4cfaf3e242b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 13:26:33 +0200 Subject: [PATCH 0450/1172] add custom sanity_check_paths in libxml2 easyconfigs --- .../libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 9 +++++++-- .../easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb | 5 +++++ 35 files changed, 177 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index aaf4c869fd..254704e224 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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-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-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index d6a8666d27..33c6ee44e2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -23,4 +23,9 @@ dependencies = [ ('Python', pythonver), ] +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-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index ddf8c95989..2cbd068791 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index e56d2ad353..2e200ff747 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index e014507e31..2e16511fc4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 833381d4b2..dd8fbb563c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 4f35163694..528265c88b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.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-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 2145f1ccf3..824084e03a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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 6e4ab86218..96f39c944c 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 @@ -4,8 +4,8 @@ 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).""" +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} @@ -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-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-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index 42fd9996e9..a36d6bdb32 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.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-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb index 232c2e480f..0c0ab111ee 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.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-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' 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 index ef442f4bb5..69506204a7 100644 --- 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 @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +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-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 5c7f304740..69319cf49a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index 3194637d11..cd4bbd99a0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index 102c2914db..3a42235cf9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 25967be117..d446d4e3c6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index 12454bc9c4..fa340e7e85 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index e2bb547666..ae74326843 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index aae9d0148e..94f3df39be 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 52ee0616b0..215198c95a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 84a2d133c6..2857dd4e54 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +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 f77fea64168d7dce85538313dffb5523bc7a257c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 15:14:10 +0200 Subject: [PATCH 0451/1172] {tools}[dummy] GC3Pie 2.2.3 --- easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb | 19 +++++++++++ .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 32 +++++++++++++++++++ .../p/PrettyTable/PrettyTable-0.7.2.eb | 20 ++++++++++++ .../easyconfigs/p/paramiko/paramiko-1.15.2.eb | 24 ++++++++++++++ .../p/parsedatetime/parsedatetime-1.4.eb | 19 +++++++++++ .../easyconfigs/p/pyCLI/pyCLI-20140329.eb | 22 +++++++++++++ .../easyconfigs/p/pycrypto/pycrypto-2.6.1.eb | 29 +++++++++++++++++ .../s/SQLAlchemy/SQLAlchemy-1.0.5.eb | 19 +++++++++++ 8 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb create mode 100644 easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb create mode 100644 easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb create mode 100644 easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb create mode 100644 easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb create mode 100644 easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb new file mode 100644 index 0000000000..f6f2a181c2 --- /dev/null +++ b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'ecdsa' +version = '0.13' + +homepage = 'http://github.com/warner/python-ecdsa' +description = """ECDSA cryptographic signature library (pure Python).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/ecdsa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb new file mode 100644 index 0000000000..cfeb39d2cd --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -0,0 +1,32 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'GC3Pie' +version = '2.2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('ecdsa', '0.13'), # required for paramiko + ('pycrypto', '2.6.1'), # required for paramiko + ('paramiko', '1.15.2'), + ('PrettyTable', '0.7.2'), + ('pyCLI', '20140329'), + ('SQLAlchemy', '1.0.5'), + ('parsedatetime', '1.4'), +] + +options = {'modulename': 'gc3libs'} + +sanity_check_paths = { + 'files': ['bin/gc3utils'], + 'dirs': ['lib/gc3utils', 'lib/gc3libs'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb new file mode 100644 index 0000000000..a75ea18716 --- /dev/null +++ b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb @@ -0,0 +1,20 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'PrettyTable' +version = '0.7.2' + +homepage = 'http://code.google.com/p/prettytable/' +description = """PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data + in visually appealing ASCII tables.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/prettytable.py'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb new file mode 100644 index 0000000000..fb4a02667b --- /dev/null +++ b/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb @@ -0,0 +1,24 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'paramiko' +version = '1.15.2' + +homepage = 'https://github.com/paramiko/paramiko/' +description = """Native Python SSHv2 protocol library""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('ecdsa', '0.13'), + ('pycrypto', '2.6.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/paramiko'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb new file mode 100644 index 0000000000..181df165c0 --- /dev/null +++ b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'parsedatetime' +version = '1.4' + +homepage = 'http://github.com/bear/parsedatetime/' +description = """Parse human-readable date/time text.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/parsedatetime'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb new file mode 100644 index 0000000000..8c1d8067dd --- /dev/null +++ b/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb @@ -0,0 +1,22 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pyCLI' +version = '20140329' + +homepage = 'http://packages.python.org/pyCLI/' +description = """Simple, object-oriented approach to Python CLI apps""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = ['pyCLI-devel.tar.gz'] +checksums = ['5cad880168f3423a1235b396735c1360'] + +options = {'modulename': 'cli'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/cli'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb new file mode 100644 index 0000000000..88292f1478 --- /dev/null +++ b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pycrypto' +version = '2.6.1' + +homepage = 'http://www.pycrypto.org/' +description = """Cryptographic modules for Python.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# install into a path that's no specific to the Python version being used +installopts = '--install-lib=%(installdir)s/lib --no-compile' + +options = {'modulename': 'Crypto'} + +modextrapaths = {'PYTHONPATH': ['lib']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/Crypto'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb new file mode 100644 index 0000000000..2354094058 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'SQLAlchemy' +version = '1.0.5' + +homepage = 'http://www.sqlalchemy.org/' +description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/sqlalchemy'], +} + +moduleclass = 'lib' -- GitLab From 6e151e945a3e87f9cc1a946a338675d617634d2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 21:17:40 +0200 Subject: [PATCH 0452/1172] {devel}[GNU-5.1.0-2.25] Autotools 20150215 --- .../Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb | 26 +++++++++++++++ .../Automake/Automake-1.15-GNU-5.1.0-2.25.eb | 33 +++++++++++++++++++ .../Autotools-20150215-GNU-5.1.0-2.25.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb | 17 ++++++++++ .../m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 23 +++++++++++++ 5 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..af0a90aedb --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..1d63ee839d --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..0d6c26a78c --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..33c6f3867e --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..e83b261924 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8e6d6384be311c371a85e662a1b07aef23826886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 21:20:00 +0200 Subject: [PATCH 0453/1172] {toolchain} gompi/2015b --- easybuild/easyconfigs/g/gompi/gompi-2015b.eb | 23 +++++++++++++ .../h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb | 23 +++++++++++++ .../numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb | 27 +++++++++++++++ .../o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb | 34 +++++++++++++++++++ 4 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015b.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb new file mode 100644 index 0000000000..a915cf4f95 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.1.0' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..c8e52b3fe3 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.1' + +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': 'GNU', 'version': '5.1.0-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..7f1c8eefc3 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +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': 'GNU', 'version': '5.1.0-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..5973ddafd1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.1')] + +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')] + +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 ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From cd7949d0e942edae147bb1b829a4f4e63ec68885 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 21:21:58 +0200 Subject: [PATCH 0454/1172] {toolchain} foss/2015b --- .../f/FFTW/FFTW-3.3.4-gompi-2015b.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2015b.eb | 39 ++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb | 18 +++++++ ...BLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb | 51 +++++++++++++++++++ ...ompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb | 25 +++++++++ 5 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2015b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.eb new file mode 100644 index 0000000000..c048de7a21 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.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': '2015b'} +toolchainopts = {'optarch': True, '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-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb new file mode 100644 index 0000000000..415cfd1a90 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015b' + +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 = '5.1.0' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# 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, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), + ('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/h/HPL/HPL-2.1-foss-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb new file mode 100644 index 0000000000..728ad9cf2e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.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': '2015b'} +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/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..a7c27b0146 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.14' + +lapackver = '3.5.0' +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': 'GNU', 'version': '5.1.0-2.25'} + +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/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..04520881ee --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.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': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GNU', '5.1.0-2.25'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 20030502f60b0018ea7f66aecd306e5c4b9688bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 21:25:08 +0200 Subject: [PATCH 0455/1172] {toolchain} intel/2015b --- .../easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb | 18 ++++++++++++++ .../i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb | 24 +++++++++++++++++++ .../iccifort-2015.3.187-GNU-5.1.0-2.25.eb | 17 +++++++++++++ .../ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb | 23 ++++++++++++++++++ .../i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb | 21 ++++++++++++++++ ...l-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb | 22 +++++++++++++++++ ....048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb | 19 +++++++++++++++ easybuild/easyconfigs/i/intel/intel-2015b.eb | 21 ++++++++++++++++ 8 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2015b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb new file mode 100644 index 0000000000..fa34ec665e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.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': '2015b'} +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-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..ab75663608 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb @@ -0,0 +1,24 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +gnu = 'GNU' +gnuver = '5.1.0-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +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-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..91b5c21fb3 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb @@ -0,0 +1,17 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' +versionsuffix = '-GNU-5.1.0-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C, C++ and Fortran compilers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..5f9e537efe --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb @@ -0,0 +1,23 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +gnu = 'GNU' +gnuver = '5.1.0-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +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-7.3.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..5ddcd4cb45 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' +versionsuffix = '-GNU-5.1.0-2.25' + +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 = '3.187' +compver = '2015.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..60bd4ce3a2 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +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': '7.3.5-GNU-5.1.0-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..8c0670293a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +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': '2015.3.187-GNU-5.1.0-2.25'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb new file mode 100644 index 0000000000..8ac5d4eba1 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2015b' + +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 = '2015.3.187' +gccsuff = '-GNU-5.1.0-2.25' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.2.3.187', '', ('iimpi', '7.3.5%s' % gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 69aefc331dd9bc2155c132b6ee81eed5819c2c55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Jun 2015 01:41:50 +0200 Subject: [PATCH 0456/1172] fix GC3Pie dependencies, add sanity check command --- .../easyconfigs/a/argparse/argparse-1.3.0.eb | 19 +++++++++++ easybuild/easyconfigs/b/Babel/Babel-1.3.eb | 21 ++++++++++++ easybuild/easyconfigs/b/boto/boto-2.9.4.eb | 19 +++++++++++ .../e/ecdsa/{ecdsa-0.13.eb => ecdsa-0.11.eb} | 10 ++++-- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 22 +++++++++---- .../easyconfigs/i/iso8601/iso8601-0.1.10.eb | 19 +++++++++++ ...{paramiko-1.15.2.eb => paramiko-1.13.0.eb} | 6 ++-- ...datetime-1.4.eb => parsedatetime-0.8.7.eb} | 2 +- easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb | 21 ++++++++++++ easybuild/easyconfigs/p/pip/pip-7.0.3.eb | 19 +++++++++++ .../{pyCLI-20140329.eb => pyCLI-2.0.3.eb} | 5 ++- .../python-novaclient-2.15.0.eb | 32 +++++++++++++++++++ easybuild/easyconfigs/p/pytz/pytz-2015.4.eb | 19 +++++++++++ .../easyconfigs/r/requests/requests-2.4.2.eb | 19 +++++++++++ ...QLAlchemy-1.0.5.eb => SQLAlchemy-0.7.9.eb} | 2 +- .../s/setuptools/setuptools-17.1.1.eb | 19 +++++++++++ .../s/simplejson/simplejson-3.7.3.eb | 19 +++++++++++ easybuild/easyconfigs/s/six/six-1.9.0.eb | 19 +++++++++++ 18 files changed, 276 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb create mode 100644 easybuild/easyconfigs/b/Babel/Babel-1.3.eb create mode 100644 easybuild/easyconfigs/b/boto/boto-2.9.4.eb rename easybuild/easyconfigs/e/ecdsa/{ecdsa-0.13.eb => ecdsa-0.11.eb} (55%) create mode 100644 easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb rename easybuild/easyconfigs/p/paramiko/{paramiko-1.15.2.eb => paramiko-1.13.0.eb} (79%) rename easybuild/easyconfigs/p/parsedatetime/{parsedatetime-1.4.eb => parsedatetime-0.8.7.eb} (95%) create mode 100644 easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb create mode 100644 easybuild/easyconfigs/p/pip/pip-7.0.3.eb rename easybuild/easyconfigs/p/pyCLI/{pyCLI-20140329.eb => pyCLI-2.0.3.eb} (78%) create mode 100644 easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb create mode 100644 easybuild/easyconfigs/p/pytz/pytz-2015.4.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.4.2.eb rename easybuild/easyconfigs/s/SQLAlchemy/{SQLAlchemy-1.0.5.eb => SQLAlchemy-0.7.9.eb} (95%) create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb create mode 100644 easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb create mode 100644 easybuild/easyconfigs/s/six/six-1.9.0.eb diff --git a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb new file mode 100644 index 0000000000..6200884242 --- /dev/null +++ b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'argparse' +version = '1.3.0' + +homepage = 'http://code.google.com/p/argparse/' +description = """Python command-line parsing library""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/argparse.py'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb new file mode 100644 index 0000000000..916af760ce --- /dev/null +++ b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb @@ -0,0 +1,21 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'Babel' +version = '1.3' + +homepage = 'http://babel.pocoo.org/' +description = """A collection of tools for internationalizing Python applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('pytz', '2015.4')] + +sanity_check_paths = { + 'files': ['bin/pybabel'], + 'dirs': ['lib/babel'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb new file mode 100644 index 0000000000..bec02fba24 --- /dev/null +++ b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'boto' +version = '2.9.4' + +homepage = 'https://github.com/boto/boto/' +description = """Boto is a Python package that provides interfaces to Amazon Web Services.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/boto'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb similarity index 55% rename from easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb rename to easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb index f6f2a181c2..0435b19fa5 100644 --- a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb +++ b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb @@ -1,7 +1,7 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'PythonPackage' name = 'ecdsa' -version = '0.13' +version = '0.11' homepage = 'http://github.com/warner/python-ecdsa' description = """ECDSA cryptographic signature library (pure Python).""" @@ -11,6 +11,12 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# install into a path that's no specific to the Python version being used +installopts = "--install-lib=%(installdir)s/lib --no-compile" + sanity_check_paths = { 'files': [], 'dirs': ['lib/ecdsa'], diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index cfeb39d2cd..a1b1ee32cd 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -7,20 +7,28 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + dependencies = [ - ('ecdsa', '0.13'), # required for paramiko + ('ecdsa', '0.11'), # required for paramiko ('pycrypto', '2.6.1'), # required for paramiko - ('paramiko', '1.15.2'), + ('paramiko', '1.13.0'), ('PrettyTable', '0.7.2'), - ('pyCLI', '20140329'), - ('SQLAlchemy', '1.0.5'), - ('parsedatetime', '1.4'), + ('pyCLI', '2.0.3'), + ('SQLAlchemy', '0.7.9'), + ('parsedatetime', '0.8.7'), + ('boto', '2.9.4'), + ('python-novaclient', '2.15.0'), ] +# make sure a sufficiently recent setuptools is used, to avoid 'DistributionNotFound' errors +# see also http://www.fabfile.org/faq.html +builddependencies = [('setuptools', '17.1.1')] options = {'modulename': 'gc3libs'} @@ -29,4 +37,6 @@ sanity_check_paths = { 'dirs': ['lib/gc3utils', 'lib/gc3libs'] } +sanity_check_commands = [('gc3utils', 'info --version')] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb new file mode 100644 index 0000000000..42dfb305fb --- /dev/null +++ b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'iso8601' +version = '0.1.10' + +homepage = 'https://bitbucket.org/micktwomey/pyiso8601/' +description = """Simple module to parse ISO 8601 dates""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/iso8601'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb similarity index 79% rename from easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb rename to easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb index fb4a02667b..ba205dd760 100644 --- a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb +++ b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb @@ -1,18 +1,18 @@ easyblock = 'VersionIndependentPythonPackage' name = 'paramiko' -version = '1.15.2' +version = '1.13.0' homepage = 'https://github.com/paramiko/paramiko/' description = """Native Python SSHv2 protocol library""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('ecdsa', '0.13'), + ('ecdsa', '0.11'), ('pycrypto', '2.6.1'), ] diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb similarity index 95% rename from easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb rename to easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb index 181df165c0..6575af2226 100644 --- a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb +++ b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'parsedatetime' -version = '1.4' +version = '0.8.7' homepage = 'http://github.com/bear/parsedatetime/' description = """Parse human-readable date/time text.""" diff --git a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb new file mode 100644 index 0000000000..2d32a2ff46 --- /dev/null +++ b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb @@ -0,0 +1,21 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pbr' +version = '0.5.21' + +homepage = 'https://launchpad.net/pbr' +description = """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('pip', '7.0.3')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/pbr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb new file mode 100644 index 0000000000..edb2a34b6f --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pip' +version = '7.0.3' + +homepage = 'https://pip.pypa.io/' +description = """he PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/pip'], + 'dirs': ['lib/pip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb similarity index 78% rename from easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb rename to easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb index 8c1d8067dd..4d71b105aa 100644 --- a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb +++ b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'pyCLI' -version = '20140329' +version = '2.0.3' homepage = 'http://packages.python.org/pyCLI/' description = """Simple, object-oriented approach to Python CLI apps""" @@ -9,8 +9,7 @@ description = """Simple, object-oriented approach to Python CLI apps""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [PYPI_SOURCE] -sources = ['pyCLI-devel.tar.gz'] -checksums = ['5cad880168f3423a1235b396735c1360'] +sources = [SOURCE_TAR_GZ] options = {'modulename': 'cli'} diff --git a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb new file mode 100644 index 0000000000..28c6db9637 --- /dev/null +++ b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb @@ -0,0 +1,32 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'python-novaclient' +version = '2.15.0' + +homepage = 'https://git.openstack.org/cgit/openstack/python-novaclient' +description = """Client library for OpenStack Compute API""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('pbr', '0.5.21'), + ('Babel', '1.3'), + ('PrettyTable', '0.7.2'), + ('simplejson', '3.7.3'), + ('requests', '2.4.2'), + ('iso8601', '0.1.10'), + ('argparse', '1.3.0'), + ('six', '1.9.0'), +] + +options = {'modulename': 'novaclient'} + +sanity_check_paths = { + 'files': ['bin/nova'], + 'dirs': ['lib/novaclient'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb new file mode 100644 index 0000000000..5bcf8c4fa0 --- /dev/null +++ b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pytz' +version = '2015.4' + +homepage = 'http://pythonhosted.org/pytz' +description = """World timezone definitions, modern and historical""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/pytz'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb new file mode 100644 index 0000000000..c3bc39cdc8 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'requests' +version = '2.4.2' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/requests'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb similarity index 95% rename from easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb rename to easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb index 2354094058..8483b950e9 100644 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'SQLAlchemy' -version = '1.0.5' +version = '0.7.9' homepage = 'http://www.sqlalchemy.org/' description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb new file mode 100644 index 0000000000..29af11dc0f --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'setuptools' +version = '17.1.1' + +homepage = 'https://pypi.python.org/pypi/setuptools/' +description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/easy_install'], + 'dirs': ['lib/setuptools'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb new file mode 100644 index 0000000000..c88c56893e --- /dev/null +++ b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'simplejson' +version = '3.7.3' + +homepage = 'http://github.com/simplejson/simplejson' +description = """Simple, fast, extensible JSON encoder/decoder for Python.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/simplejson'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/six/six-1.9.0.eb b/easybuild/easyconfigs/s/six/six-1.9.0.eb new file mode 100644 index 0000000000..a91199175e --- /dev/null +++ b/easybuild/easyconfigs/s/six/six-1.9.0.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'six' +version = '1.9.0' + +homepage = 'http://pypi.python.org/pypi/six' +description = """Python 2 and 3 compatibility utilities""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/six.py'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 64c1bc883c738279450d399c8ae0349920a35731 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 13:41:53 +0200 Subject: [PATCH 0457/1172] install GC3Pie as a bundle of Python packages --- .../easyconfigs/a/argparse/argparse-1.3.0.eb | 19 ------- easybuild/easyconfigs/b/Babel/Babel-1.3.eb | 21 ------- easybuild/easyconfigs/b/boto/boto-2.9.4.eb | 19 ------- easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb | 25 --------- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 55 ++++++++++++------- .../easyconfigs/i/iso8601/iso8601-0.1.10.eb | 19 ------- .../p/PrettyTable/PrettyTable-0.7.2.eb | 20 ------- .../easyconfigs/p/paramiko/paramiko-1.13.0.eb | 24 -------- .../p/parsedatetime/parsedatetime-0.8.7.eb | 19 ------- easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb | 21 ------- easybuild/easyconfigs/p/pip/pip-7.0.3.eb | 19 ------- easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb | 21 ------- .../easyconfigs/p/pycrypto/pycrypto-2.6.1.eb | 29 ---------- .../python-novaclient-2.15.0.eb | 32 ----------- easybuild/easyconfigs/p/pytz/pytz-2015.4.eb | 19 ------- .../easyconfigs/r/requests/requests-2.4.2.eb | 19 ------- .../s/SQLAlchemy/SQLAlchemy-0.7.9.eb | 19 ------- .../s/setuptools/setuptools-17.1.1.eb | 19 ------- .../s/simplejson/simplejson-3.7.3.eb | 19 ------- easybuild/easyconfigs/s/six/six-1.9.0.eb | 19 ------- 20 files changed, 36 insertions(+), 421 deletions(-) delete mode 100644 easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb delete mode 100644 easybuild/easyconfigs/b/Babel/Babel-1.3.eb delete mode 100644 easybuild/easyconfigs/b/boto/boto-2.9.4.eb delete mode 100644 easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb delete mode 100644 easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb delete mode 100644 easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb delete mode 100644 easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb delete mode 100644 easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb delete mode 100644 easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb delete mode 100644 easybuild/easyconfigs/p/pip/pip-7.0.3.eb delete mode 100644 easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb delete mode 100644 easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb delete mode 100644 easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb delete mode 100644 easybuild/easyconfigs/p/pytz/pytz-2015.4.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.4.2.eb delete mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb delete mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb delete mode 100644 easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb delete mode 100644 easybuild/easyconfigs/s/six/six-1.9.0.eb diff --git a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb deleted file mode 100644 index 6200884242..0000000000 --- a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'argparse' -version = '1.3.0' - -homepage = 'http://code.google.com/p/argparse/' -description = """Python command-line parsing library""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/argparse.py'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb deleted file mode 100644 index 916af760ce..0000000000 --- a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'Babel' -version = '1.3' - -homepage = 'http://babel.pocoo.org/' -description = """A collection of tools for internationalizing Python applications.""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('pytz', '2015.4')] - -sanity_check_paths = { - 'files': ['bin/pybabel'], - 'dirs': ['lib/babel'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb deleted file mode 100644 index bec02fba24..0000000000 --- a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'boto' -version = '2.9.4' - -homepage = 'https://github.com/boto/boto/' -description = """Boto is a Python package that provides interfaces to Amazon Web Services.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/boto'], - 'dirs': ['bin'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb deleted file mode 100644 index 0435b19fa5..0000000000 --- a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ecdsa' -version = '0.11' - -homepage = 'http://github.com/warner/python-ecdsa' -description = """ECDSA cryptographic signature library (pure Python).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# allow use of system Python -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -# install into a path that's no specific to the Python version being used -installopts = "--install-lib=%(installdir)s/lib --no-compile" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/ecdsa'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index a1b1ee32cd..900ad6b418 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -1,4 +1,4 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'Bundle' name = 'GC3Pie' version = '2.2.3' @@ -7,34 +7,51 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -dependencies = [ - ('ecdsa', '0.11'), # required for paramiko - ('pycrypto', '2.6.1'), # required for paramiko - ('paramiko', '1.13.0'), - ('PrettyTable', '0.7.2'), - ('pyCLI', '2.0.3'), - ('SQLAlchemy', '0.7.9'), - ('parsedatetime', '0.8.7'), - ('boto', '2.9.4'), - ('python-novaclient', '2.15.0'), +ext_options = { + 'source_urls': [PYPI_LOWER_SOURCE], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', +} + +exts_list = [ + ('setuptools', '17.1.1', ext_options), + ('ecdsa', '0.11', ext_options), # required for paramiko + ('pycrypto', '2.6.1', dict(ext_options.items() + [('modulename', 'Crypto')])), # required for paramiko + ('paramiko', '1.13.0', ext_options), + ('PrettyTable', '0.7.2', dict(ext_options.items() + [('source_tmpl', 'prettytable-%(version)s.tar.gz')])), + ('pyCLI', '2.0.3', dict(ext_options.items() + [('modulename', 'cli')])), + ('SQLAlchemy', '0.7.9', ext_options), + ('parsedatetime', '0.8.7', ext_options), + ('boto', '2.9.4', ext_options), + ('pip', '7.0.3'), # required for pbr + ('pbr', '0.11.0'), # required for python-novaclient + ('Babel', '1.3'), # required for python-novaclient + ('simplejson', '3.7.3'), # required for python-novaclient + ('requests', '2.4.2'), # required for python-novaclient + ('iso8601', '0.1.10'), # required for python-novaclient + ('argparse', '1.3.0'), # required for python-novaclient + ('six', '1.9.0'), # required for python-novaclient + ('python-novaclient', '2.15.0', dict(ext_options.items() + [('modulename', 'novaclient')])), + (name.lower(), version, dict(ext_options.items() + [('modulename', 'gc3libs')])), ] -# make sure a sufficiently recent setuptools is used, to avoid 'DistributionNotFound' errors -# see also http://www.fabfile.org/faq.html -builddependencies = [('setuptools', '17.1.1')] -options = {'modulename': 'gc3libs'} +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': ['lib/gc3utils', 'lib/gc3libs'] + 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb deleted file mode 100644 index 42dfb305fb..0000000000 --- a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'iso8601' -version = '0.1.10' - -homepage = 'https://bitbucket.org/micktwomey/pyiso8601/' -description = """Simple module to parse ISO 8601 dates""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/iso8601'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb deleted file mode 100644 index a75ea18716..0000000000 --- a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'PrettyTable' -version = '0.7.2' - -homepage = 'http://code.google.com/p/prettytable/' -description = """PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data - in visually appealing ASCII tables.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/prettytable.py'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb deleted file mode 100644 index ba205dd760..0000000000 --- a/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'paramiko' -version = '1.13.0' - -homepage = 'https://github.com/paramiko/paramiko/' -description = """Native Python SSHv2 protocol library""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('ecdsa', '0.11'), - ('pycrypto', '2.6.1'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/paramiko'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb deleted file mode 100644 index 6575af2226..0000000000 --- a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'parsedatetime' -version = '0.8.7' - -homepage = 'http://github.com/bear/parsedatetime/' -description = """Parse human-readable date/time text.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/parsedatetime'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb deleted file mode 100644 index 2d32a2ff46..0000000000 --- a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pbr' -version = '0.5.21' - -homepage = 'https://launchpad.net/pbr' -description = """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('pip', '7.0.3')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/pbr'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb deleted file mode 100644 index edb2a34b6f..0000000000 --- a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pip' -version = '7.0.3' - -homepage = 'https://pip.pypa.io/' -description = """he PyPA recommended tool for installing Python packages.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/pip'], - 'dirs': ['lib/pip'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb deleted file mode 100644 index 4d71b105aa..0000000000 --- a/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pyCLI' -version = '2.0.3' - -homepage = 'http://packages.python.org/pyCLI/' -description = """Simple, object-oriented approach to Python CLI apps""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -options = {'modulename': 'cli'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/cli'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb deleted file mode 100644 index 88292f1478..0000000000 --- a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pycrypto' -version = '2.6.1' - -homepage = 'http://www.pycrypto.org/' -description = """Cryptographic modules for Python.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# allow use of system Python -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -# install into a path that's no specific to the Python version being used -installopts = '--install-lib=%(installdir)s/lib --no-compile' - -options = {'modulename': 'Crypto'} - -modextrapaths = {'PYTHONPATH': ['lib']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/Crypto'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb deleted file mode 100644 index 28c6db9637..0000000000 --- a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'python-novaclient' -version = '2.15.0' - -homepage = 'https://git.openstack.org/cgit/openstack/python-novaclient' -description = """Client library for OpenStack Compute API""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('pbr', '0.5.21'), - ('Babel', '1.3'), - ('PrettyTable', '0.7.2'), - ('simplejson', '3.7.3'), - ('requests', '2.4.2'), - ('iso8601', '0.1.10'), - ('argparse', '1.3.0'), - ('six', '1.9.0'), -] - -options = {'modulename': 'novaclient'} - -sanity_check_paths = { - 'files': ['bin/nova'], - 'dirs': ['lib/novaclient'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb deleted file mode 100644 index 5bcf8c4fa0..0000000000 --- a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pytz' -version = '2015.4' - -homepage = 'http://pythonhosted.org/pytz' -description = """World timezone definitions, modern and historical""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/pytz'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb deleted file mode 100644 index c3bc39cdc8..0000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'requests' -version = '2.4.2' - -homepage = 'https://pypi.python.org/pypi/requests' -description = """Python http for humans""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/requests'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb deleted file mode 100644 index 8483b950e9..0000000000 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'SQLAlchemy' -version = '0.7.9' - -homepage = 'http://www.sqlalchemy.org/' -description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/sqlalchemy'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb deleted file mode 100644 index 29af11dc0f..0000000000 --- a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'setuptools' -version = '17.1.1' - -homepage = 'https://pypi.python.org/pypi/setuptools/' -description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/easy_install'], - 'dirs': ['lib/setuptools'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb deleted file mode 100644 index c88c56893e..0000000000 --- a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'simplejson' -version = '3.7.3' - -homepage = 'http://github.com/simplejson/simplejson' -description = """Simple, fast, extensible JSON encoder/decoder for Python.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/simplejson'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/six/six-1.9.0.eb b/easybuild/easyconfigs/s/six/six-1.9.0.eb deleted file mode 100644 index a91199175e..0000000000 --- a/easybuild/easyconfigs/s/six/six-1.9.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'six' -version = '1.9.0' - -homepage = 'http://pypi.python.org/pypi/six' -description = """Python 2 and 3 compatibility utilities""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/six.py'], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From d3d531982170ea29b4d5cc5dbd643074f990e2c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 14:06:46 +0200 Subject: [PATCH 0458/1172] fix source_urls for GC3Pie easyconfig --- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 96 ++++++++++++++----- 1 file changed, 72 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index 900ad6b418..e3154cc1a9 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -16,31 +16,79 @@ exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -ext_options = { - 'source_urls': [PYPI_LOWER_SOURCE], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', -} - exts_list = [ - ('setuptools', '17.1.1', ext_options), - ('ecdsa', '0.11', ext_options), # required for paramiko - ('pycrypto', '2.6.1', dict(ext_options.items() + [('modulename', 'Crypto')])), # required for paramiko - ('paramiko', '1.13.0', ext_options), - ('PrettyTable', '0.7.2', dict(ext_options.items() + [('source_tmpl', 'prettytable-%(version)s.tar.gz')])), - ('pyCLI', '2.0.3', dict(ext_options.items() + [('modulename', 'cli')])), - ('SQLAlchemy', '0.7.9', ext_options), - ('parsedatetime', '0.8.7', ext_options), - ('boto', '2.9.4', ext_options), - ('pip', '7.0.3'), # required for pbr - ('pbr', '0.11.0'), # required for python-novaclient - ('Babel', '1.3'), # required for python-novaclient - ('simplejson', '3.7.3'), # required for python-novaclient - ('requests', '2.4.2'), # required for python-novaclient - ('iso8601', '0.1.10'), # required for python-novaclient - ('argparse', '1.3.0'), # required for python-novaclient - ('six', '1.9.0'), # required for python-novaclient - ('python-novaclient', '2.15.0', dict(ext_options.items() + [('modulename', 'novaclient')])), - (name.lower(), version, dict(ext_options.items() + [('modulename', 'gc3libs')])), + ('setuptools', '17.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '0.7.9', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '0.8.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.9.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.15.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), ] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) -- GitLab From f62823897b177a93a09d8b194df90b08063f2b32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 16:12:30 +0200 Subject: [PATCH 0459/1172] include both lib and lib64 in $PYTHONPATH in GC3Pie easyconfig --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index e3154cc1a9..d8254ca575 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -93,7 +93,8 @@ exts_list = [ pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver]} full_sanity_check = True -- GitLab From a26edced5925bc4ea05e4c7fe363c432d1989200 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 16:27:28 +0200 Subject: [PATCH 0460/1172] fix source_urls for argparse Python extension --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 2 +- 47 files changed, 47 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 08ae2a5f52..aa976378fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 5691adf05e..1977d33177 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 8bf00ee94a..b82404eb26 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 2ade7ad4f1..0eaf32ef4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a73fef035d..aeb1a5dbe8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 2af2f0c181..5708c09083 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 0218dcafbd..d0197126f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 342b19c101..2c3b844cef 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index b883b3a7a7..d2fb8dbf98 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 53fb8ff292..8af79fb950 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index c2cc52183e..4715f5d29d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 994f20889f..9e8e258f1e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 459199e8c5..4ea3681947 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 3e4b4f03f3..055d5c5563 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 2e8be6d925..8e32b0f084 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index c6d6010f0e..77656f8d16 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 2da448273b..ad5369bd07 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index b7849aec58..bbc8eab1c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index c17df2cb09..6186a3614b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 9f5cd7d95f..e943c91436 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 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 a24d0b3e6e..b2b682da04 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 @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index cee2b8e189..09ce3003e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 751a483994..ea85f15f15 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 8b46b16cd3..c14fdff5ce 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index ed13d94285..23aec43a01 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -56,7 +56,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 8e7a62f6da..42b742d915 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index aaba09ba09..3cc492d6b4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index d9f7ad0b77..0c53db7e43 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 6e042b928d..31ea2a894b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 09dc45c1e6..5c19bcd953 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], 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 383b7d978b..f1ec579fbe 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 @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 18aa12a4b8..b620899273 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 787f5ecab1..1ae3ec0c5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 16a9eea25f..60923e701c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 39d6b11c34..2e085966c7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index 466ad2cc0c..0c1b139dda 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 5a66cda69a..186e5f94df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index d0661c356d..e5b95d6f14 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index cc0e90d0e3..bb297e5eb8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index bb0fac1650..27281d943c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index ed4d77fc45..2c04d1e9a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 033d183105..66a6b2687c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index c928dc3ca3..ce554428cd 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index f523509a1d..3e3d09b0be 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index a47ee809f5..98228f8b19 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index d3f83f3c59..b7690d84fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -61,7 +61,7 @@ exts_list = [ ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 9f71e6e86f..91935078a9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -61,7 +61,7 @@ exts_list = [ ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], -- GitLab From 7bc30033e5b9c5015c0c8a2e96912b8fb99ab18d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 17:35:47 +0200 Subject: [PATCH 0461/1172] fix source_urls for deap Python extension --- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index b82404eb26..b447f3f5c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 0eaf32ef4a..3b9b9b0071 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index aeb1a5dbe8..e9411a98a0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 5708c09083..9d81cee86b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index d0197126f1..b7dfb64df9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 2c3b844cef..5eb4c88938 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index d2fb8dbf98..878951cc6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 8af79fb950..957d719fbd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 4715f5d29d..49da1ce96f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 9e8e258f1e..ff029a2234 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 4ea3681947..2ef8f9fc88 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 055d5c5563..b5075a6a9a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 8e32b0f084..e1bc68f6d1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 77656f8d16..1f6678ca73 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index ad5369bd07..bcc80770f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index bbc8eab1c5..262801c6c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 6186a3614b..7713f86879 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -71,7 +71,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index e943c91436..0acac864f5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 b2b682da04..b8e12d524c 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 @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 09ce3003e9..9fda7777e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index ea85f15f15..6f7edf431e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index c14fdff5ce..3c2a47e51e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 23aec43a01..c8797b36e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -72,7 +72,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 42b742d915..de11eaf356 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 3cc492d6b4..b8f2f71c12 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 0c53db7e43..be1053a62d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 31ea2a894b..caf05b2cc7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 66a6b2687c..ddf1d2d853 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index ce554428cd..86066e4a5e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index 3e3d09b0be..b01168b83e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 98228f8b19..de9617eacf 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], -- GitLab From 71581ecabb33f908cf4e6f1b50bdc5d3f1e65ac8 Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 14:49:30 +0200 Subject: [PATCH 0462/1172] .eb file for Bowtie2-2.2.5-goolf-1.7.20 --- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..30dfc18960 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.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: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +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': 'goolf', 'version': '1.7.20'} + +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 46d48a8687599e68e33e1ec5f9b06cab652a3a60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jun 2015 15:12:00 +0200 Subject: [PATCH 0463/1172] {vis}[*/2015a] Pillow 2.8.1 --- .../Pillow-2.8.1-foss-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ .../Pillow-2.8.1-intel-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..524dd9ba3d --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +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': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..04c7f0efa3 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 9eb0080c3f24d806d39f0ddf887797bebd53107a Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 17:56:59 +0200 Subject: [PATCH 0464/1172] .eb file for Python-2.7.9-goolf-1.7.20 --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..324a98e966 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,119 @@ +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': '1.7.20'} +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'), +# ('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 = [ + ('requests', '2.6.2', { + 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], + }), + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://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': ['http://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': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('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': ['http://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' -- GitLab From 3d6004535fc3ea4f6c85df920b2f0ce2c039f45b Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 18:15:24 +0200 Subject: [PATCH 0465/1172] .eb file for Ghostscript-9.16-goolf-1.7.2 --- .../Ghostscript-9.16-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb new file mode 100644 index 0000000000..270e7df776 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.16' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +# expat, freetype and libpng are optional deps, +# these are actually patched and included in the sources, +dependencies = [ + ('LibTIFF', '4.0.3'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' -- GitLab From 0327feff827d5a017ad8322f9e2e76bd6d51a07f Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 18:17:26 +0200 Subject: [PATCH 0466/1172] .eb file for LibTIFF-4.0.3-goolf-1.7.20 --- .../l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..46a3c3ee49 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 343db5ac56707f338adc6b7a1a0aef48ba2d2d93 Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 20:20:27 +0200 Subject: [PATCH 0467/1172] .eb for libgtextutils-0.6.1-goolf-1.7.2 --- .../libgtextutils-0.6.1-goolf-1.7.20.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..89f72fe364 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.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:: 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 = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } + +moduleclass = 'bio' -- GitLab From b69ab3196178cebcada2c3387dc4ee9b9692d176 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 07:48:43 +0200 Subject: [PATCH 0468/1172] fix easyconfigs unit tests after making ModulesTool a non-singleton class (cfr. https://github.com/hpcugent/easybuild-framework/pull/1299) --- test/easyconfigs/easyconfigs.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6efa3b178f..12d11afc1e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -32,6 +32,7 @@ import copy import glob import os import re +import shutil import sys import tempfile from distutils.version import LooseVersion @@ -48,6 +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.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool @@ -79,10 +81,10 @@ class EasyConfigTest(TestCase): config.set_tmpdir() del eb_go - # mock 'exist' and 'load' methods of modules tool, which are used for 'craype' external module - modtool = modules_tool() - modtool.exist = lambda m: [True]*len(m) - modtool.load = lambda m: True + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = TMPDIR + write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n') log = fancylogger.getLogger("EasyConfigTest", fname=False) @@ -227,6 +229,10 @@ class EasyConfigTest(TestCase): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + def test_zzz_cleanup(self): + """Dummy test to clean up global temporary directory.""" + shutil.rmtree(self.TMPDIR) + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" -- GitLab From 5da2cf5a61420352c9cb9ef290abdbd3c413a929 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 3 Jun 2015 13:15:57 +0200 Subject: [PATCH 0469/1172] Add support for R pbd. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 +++++++++++++++++++ ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb create mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb new file mode 100644 index 0000000000..05e79faaa5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'R-bundle' +version = '20150605' +bundlename = 'pbd' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000..ae54615b78 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + -- GitLab From e86709617e63f62a0de934294f6ebce461571c82 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 10:21:50 +0200 Subject: [PATCH 0470/1172] Use SOURCEFORGE_SOURCE as source urls, remove import time and seconds from epoch --- easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 5 +---- easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb index 6278b4ba19..72296e698f 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb @@ -1,5 +1,3 @@ -import time - easyblock = 'PackedBinary' name = 'snpEff' @@ -17,8 +15,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -seconds_after_epoch = int(time.time()) -source_urls = [('http://downloads.sourceforge.net/project/%s?ts=%s&use_mirror=autoselect' % (name.lower(), seconds_after_epoch))] +source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] checksums = ['f4571413833df913261ff76b6f40bb76'] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb index 7763b7baad..7e0c5d595f 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb @@ -1,5 +1,3 @@ -import time - easyblock = 'PackedBinary' name = 'snpEff' @@ -17,8 +15,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -seconds_after_epoch = int(time.time()) -source_urls = ['http://downloads.sourceforge.net/project/%(name.lower())s?ts=%(seconds_after_epoch)s&use_mirror=autoselect'] +source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] -- GitLab From a5f6037e278342781100925ffcfd1708806e9424 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 10:23:44 +0200 Subject: [PATCH 0471/1172] removed first empty line --- easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb index ceb5083895..cb7232a3fb 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -1,4 +1,3 @@ - name = 'SAMtools' version = '0.1.19' -- GitLab From 382c292d5f92e4f79336b446c5e2d579000101e8 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 10:48:00 +0200 Subject: [PATCH 0472/1172] Change v to in filename --- .../s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 28 +++++++++++++++++++ .../s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..72296e698f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000..7e0c5d595f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a7b9d66efdc3eca679266dc6c772fce3db0ac74f Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 11:06:40 +0200 Subject: [PATCH 0473/1172] remove snpEff files with wrong file name --- .../s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 28 ------------------- .../s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 28 ------------------- 2 files changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb delete mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb deleted file mode 100644 index 72296e698f..0000000000 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'snpEff' -version = '3.6' - -homepage = 'http://sourceforge.net/projects/snpeff/' -description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] - -source_urls = [SOURCEFORGE_SOURCE] -sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] - -checksums = ['f4571413833df913261ff76b6f40bb76'] - -sanity_check_paths = { - 'files': ['snpEff.jar', 'SnpSift.jar'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb deleted file mode 100644 index 7e0c5d595f..0000000000 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'snpEff' -version = '4.1d' - -homepage = 'http://sourceforge.net/projects/snpeff/' -description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] - -source_urls = [SOURCEFORGE_SOURCE] -sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] - -checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] - -sanity_check_paths = { - 'files': ['snpEff.jar', 'SnpSift.jar'], - 'dirs': [] -} - -moduleclass = 'bio' -- GitLab From b60a9309274819261ed452d19547dad4dbe1d372 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:01:04 +0200 Subject: [PATCH 0474/1172] Change http to https --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 324a98e966..a97b98d87d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.9' -homepage = 'http://python.org/' +homepage = 'https://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'} @@ -10,7 +10,7 @@ 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/'] +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package @@ -30,34 +30,34 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - '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')], + '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': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://argparse.googlecode.com/files/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -66,14 +66,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://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': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + '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/'], @@ -87,7 +87,7 @@ 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 5287f6181d6772f1c1819828b44363e40721c332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 12:01:41 +0200 Subject: [PATCH 0475/1172] fix remark --- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 1 + .../easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index d8254ca575..8bb06bd90a 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -96,6 +96,7 @@ pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) # on RHEL-based systems, some extensions get installed to lib, some to lib64 modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/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 = { diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb new file mode 100644 index 0000000000..00e503af1d --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'GC3Pie' +version = '2.3.dev' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# svn checkout http://gc3pie.googlecode.com/svn/trunk/ gc3pie +# gc3pie-2.3.dev.tar.gz gc3pie +sources = ['gc3pie-%(version)s.tar.gz'] + +start_dir = 'gc3pie' + +# allow use of system python +allow_system_deps = [('python', SYS_PYTHON_VERSION)] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +options = {'modulename': 'gc3libs'} + +sanity_check_paths = { + 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From b19f9deee3096685d3dfe64efc100be00608f6b7 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:12:51 +0200 Subject: [PATCH 0476/1172] fix indentation --- .../l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb index 89f72fe364..bf0770fd9f 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -24,8 +24,8 @@ sources = [SOURCE_TAR_BZ2] source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { - 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], - 'dirs': ['lib/pkgconfig'] - } + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } moduleclass = 'bio' -- GitLab From 3ffb595dca2f58b7acb26998ef621d0039ad56ec Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:16:24 +0200 Subject: [PATCH 0477/1172] Add extra dependencies --- .../g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 270e7df776..85c9d54c28 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -13,10 +13,16 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] -# expat, freetype and libpng are optional deps, -# these are actually patched and included in the sources, dependencies = [ + ('freetype', '2.5.3'), + ('fontconfig', '2.11.1'), + ('GLib', '2.40.0'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('expat', '2.1.0'), + ('cairo', '1.12.18'), ('LibTIFF', '4.0.3'), + ('zlib', '1.2.8'), ] configopts = "--with-system-libtiff --enable-dynamic" -- GitLab From 2959ff50bbdf1d5a60aafedcea5419e590891c47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 12:17:37 +0200 Subject: [PATCH 0478/1172] remove easyconfig for GC3Pie dev version that crept in --- .../easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb deleted file mode 100644 index 00e503af1d..0000000000 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'GC3Pie' -version = '2.3.dev' - -homepage = 'https://gc3pie.readthedocs.org' -description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution - environments.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# svn checkout http://gc3pie.googlecode.com/svn/trunk/ gc3pie -# gc3pie-2.3.dev.tar.gz gc3pie -sources = ['gc3pie-%(version)s.tar.gz'] - -start_dir = 'gc3pie' - -# allow use of system python -allow_system_deps = [('python', SYS_PYTHON_VERSION)] - -pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) - -options = {'modulename': 'gc3libs'} - -sanity_check_paths = { - 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], - 'dirs': [], -} - -sanity_check_commands = [('gc3utils', 'info --version')] - -moduleclass = 'tools' -- GitLab From 3ede896bf3f92cb21ea29b711bbde0c1cb613895 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:18:54 +0200 Subject: [PATCH 0479/1172] Change dependencies to include SQLite and OpenSSL and remove requests --- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index a97b98d87d..b70766f54b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('SQLite', '3.8.8.1'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + ('SQLite', '3.8.8.1'), + ('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 ] @@ -29,9 +29,6 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Jan 19th 2015 exts_list = [ - ('requests', '2.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), ('setuptools', '11.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), -- GitLab From c7ea46925714e7124d9f72285eec965faa1c65c4 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:33:39 +0200 Subject: [PATCH 0480/1172] .eb file for freetype-2.5.3-goolf-1.7.20 --- .../f/freetype/freetype-2.5.3-goolf-1.7.20 | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 new file mode 100644 index 0000000000..c5fb92d43c --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.3' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.12')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From 3aa0e15b4991d912c3677cf371853581abd076ec Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:35:26 +0200 Subject: [PATCH 0481/1172] remove Python-2.7.9-goolf-1.7.20.eb should be in Python branch --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ------------------ 1 file changed, 119 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb deleted file mode 100644 index 324a98e966..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ /dev/null @@ -1,119 +0,0 @@ -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': '1.7.20'} -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'), -# ('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 = [ - ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], - }), - ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['http://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': ['http://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': ['http://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], - }), - ('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': ['http://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' -- GitLab From 350e1cd24f06f950b485e858e01aa86207116a47 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:37:50 +0200 Subject: [PATCH 0482/1172] .eb file for fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig/fontconfig-2.11.1-goolf-1.7.20 | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 new file mode 100644 index 0000000000..e77da2e1fe --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 5bf3948c1002e8da79db7570c71e4923ded83b00 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:38:38 +0200 Subject: [PATCH 0483/1172] remove Python-2.7.9-goolf-1.7.20.eb should be in Python branch --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ------------------ 1 file changed, 119 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb deleted file mode 100644 index 324a98e966..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ /dev/null @@ -1,119 +0,0 @@ -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': '1.7.20'} -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'), -# ('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 = [ - ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], - }), - ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['http://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': ['http://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': ['http://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], - }), - ('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': ['http://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' -- GitLab From 30c2d6d35b0d54b4c932db203b14d885178e883c Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:42:28 +0200 Subject: [PATCH 0484/1172] .eb file for GLib-2.40.0-goolf-1.7.20 --- .../g/GLib/GLib-2.40.0-goolf-1.7.20.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8949f8ac3a --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.40.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From f93360c72fd77663ebe0ee8013b5017601a33eee Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:47:37 +0200 Subject: [PATCH 0485/1172] .eb file for libjpeg-turbo-1.3.1-goolf-1.7.20 --- .../libjpeg-turbo-1.3.1-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..d2b54d01ff --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +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': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' -- GitLab From eaed5bdeb7560fee2512f81dcdf392af636ee352 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:49:45 +0200 Subject: [PATCH 0486/1172] .eb file for libpng-1.6.12-goolf-1.7.20 --- .../l/libpng/libpng-1.6.12-goolf-1.7.20.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb new file mode 100644 index 0000000000..11dd528148 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From db1282d0ea7f4feddc302d76930ec0ec3ab07494 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:52:18 +0200 Subject: [PATCH 0487/1172] .eb file for expat-2.1.0-goolf-1.7.20 --- .../e/expat/expat-2.1.0-goolf-1.7.20.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..721806cde9 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From 599c5fd5a3b3c02e07eda23489d9cf3f04bdd479 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:54:26 +0200 Subject: [PATCH 0488/1172] .eb file for cairo-1.12.18-goolf-1.7.20 --- .../c/cairo/cairo-1.12.18-goolf-1.7.20.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb new file mode 100644 index 0000000000..e57987a01a --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.12'), + ('freetype', '2.5.3'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +# 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' -- GitLab From abed07bf25b3ed1216f0e985e9bb3d3dc0a07a88 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 13:31:32 +0200 Subject: [PATCH 0489/1172] The demo package is updated every 2-3 months, i.e., a checksum doesn't make much sense --- .../easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb index 42c77ab311..4151c18955 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb @@ -27,10 +27,6 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] -checksums = [ - '09cf28650be36516613372c8a0d1c0d8', # vampir-8.4.1-demo-linux-x86_64-setup.bin -] - install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { -- GitLab From 8acb4772bfc7299afe940f911afc253c162e080c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 13:36:37 +0200 Subject: [PATCH 0490/1172] Don't use ALL_CAPS: VAMPIR -> Vampir --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb | 2 +- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 2 +- .../easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb index 4151c18955..e474d1fc46 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb @@ -18,7 +18,7 @@ versionsuffix = "-demo" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index ffb4fc26ad..cdf8d18bde 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -17,7 +17,7 @@ version = "8.4.1" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 83d53b0104..29d61b1985 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -17,7 +17,7 @@ version = "8.4.1" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -- GitLab From 4a625e3c6f38f759c328a87bdb24ed1feae1e4ab Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 14:03:49 +0200 Subject: [PATCH 0491/1172] add blank line, left align } --- .../l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb index bf0770fd9f..b5f853d5af 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -17,6 +17,7 @@ version = '0.6.1' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,6 +27,6 @@ source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], 'dirs': ['lib/pkgconfig'] - } +} moduleclass = 'bio' -- GitLab From 5ab1597eda0f040aa4373a00c821d64a575d80f1 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:14:18 +0200 Subject: [PATCH 0492/1172] add cairo dependency pixman 0.32.6-goolf-1.7.20 --- .../p/pixman/pixman-0.32.6-goolf-1.7.20.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..9a915bad5f --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 227baad9b58bb155262a1e8fde9878c1c0307c7a Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:16:11 +0200 Subject: [PATCH 0493/1172] add .eb to fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig-2.11.1-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..e77da2e1fe --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 746c409b9aa762b589b1127f235ec9f378569977 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:17:34 +0200 Subject: [PATCH 0494/1172] remove fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig/fontconfig-2.11.1-goolf-1.7.20 | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 deleted file mode 100644 index e77da2e1fe..0000000000 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "fontconfig" -version = '2.11.1' - -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': 'goolf', 'version': '1.7.20'} - -source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('expat', '2.1.0'), - ('freetype','2.5.3'), -] - -configopts = '--disable-docs ' - -moduleclass = 'vis' -- GitLab From 38a40b4be0f4f7f3ba8c6cd231365a3eb7e908f1 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:32:18 +0200 Subject: [PATCH 0495/1172] Add dependency NASM-2.11.05-goolf-1.7.20.eb --- .../n/NASM/NASM-2.11.05-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb new file mode 100644 index 0000000000..61250ef0ab --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +## +# 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 = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 8ca3279b83d5e25abc8451cdd1150ce552036c8e Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:35:08 +0200 Subject: [PATCH 0496/1172] add .eb after file --- ...freetype-2.5.3-goolf-1.7.20 => freetype-2.5.3-goolf-1.7.20.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.5.3-goolf-1.7.20 => freetype-2.5.3-goolf-1.7.20.eb} (100%) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 rename to easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb -- GitLab From af6a2df0801cd6a584db168354831ca22b1fd34b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 14:39:15 +0200 Subject: [PATCH 0497/1172] Use minimal toolchains --- .../{Vampir-8.4.1-demo-foss-2015a.eb => Vampir-8.4.1-demo.eb} | 2 +- .../v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1.eb} | 2 +- ...er-8.4.1-foss-2015a.eb => VampirServer-8.4.1-gompi-2015a.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-demo-foss-2015a.eb => Vampir-8.4.1-demo.eb} (96%) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1.eb} (96%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-foss-2015a.eb => VampirServer-8.4.1-gompi-2015a.eb} (96%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb similarity index 96% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index e474d1fc46..62ddb26846 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -23,7 +23,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb similarity index 96% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index cdf8d18bde..379ca0d9f4 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -22,7 +22,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s-%s-setup.bin' % (version, variant)] diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb similarity index 96% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index 29d61b1985..b3fef1121f 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -22,7 +22,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'gompi', 'version': '2015a'} toolchainopts = {"usempi": True} sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] -- GitLab From 360d993e07be8da6e836a20374acf372d2999c35 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 14:54:03 +0200 Subject: [PATCH 0498/1172] few changes from @boegel his comments --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index b70766f54b..2eabb347c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('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 ] @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['https://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/ '], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -63,7 +63,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['https://www.cython.org/release/'], + 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], -- GitLab From f591d8b70dac8679ba3b60ba2c9d84b71cad2616 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:57:15 +0200 Subject: [PATCH 0499/1172] add depedency SQLite-3.8.8.1-goolf-1.7.20.eb --- .../s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..ee10abf948 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.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': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.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' -- GitLab From 92e0aaa1cfae7791c39f4fa8a306e2814a608b00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:03:06 +0200 Subject: [PATCH 0500/1172] fix remarks w.r.t. missing comments --- .../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 | 1 + .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 1 + .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 1 + .../easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 1 + 6 files changed, 8 insertions(+) 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 cb9289d4be..6b906969bb 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 @@ -12,7 +12,9 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + # 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) ] 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 8aefcfeeee..3b30b6d478 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 @@ -11,6 +11,7 @@ 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 = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib 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 fa4ce3cee9..e8d57cd578 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 @@ -12,7 +12,9 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + # 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) ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 3c7395c4a9..aa312b1626 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +# zlib required, but being linked instatically, so not a runtime dep builddependencies = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 3f419579d9..71c0cc0f49 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} 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 = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index d10f6ce0ce..797739b09a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} 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 = { -- GitLab From e6df0d70a70b150a71dd547594c0e451c8155c43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:17:50 +0200 Subject: [PATCH 0501/1172] fix Xmipp easyconfigs: naming, patches, deps + add foss/2015a equivalent --- .../Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ ... => Xmipp-3.1-intel-2015a-Python-2.7.9.eb} | 13 ++++++-- ...h => Xmipp-3.1_fix-library-includes.patch} | 0 ...ch => Xmipp-3.1_fix-sqlite-includes.patch} | 0 .../x/Xmipp/Xmipp_install-script.patch | 13 ++++++++ 5 files changed, 55 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb rename easybuild/easyconfigs/x/Xmipp/{Xmipp-3.1-intel-2015a.eb => Xmipp-3.1-intel-2015a-Python-2.7.9.eb} (64%) rename easybuild/easyconfigs/x/Xmipp/{library_imports.patch => Xmipp-3.1_fix-library-includes.patch} (100%) rename easybuild/easyconfigs/x/Xmipp/{sqlite_imports.patch => Xmipp-3.1_fix-sqlite-includes.patch} (100%) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..3d82992342 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +name = 'Xmipp' +version = '3.1' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Java', '1.8.0_40', '', True), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py + ('LibTIFF', '4.0.4beta'), + ('HDF5', '1.8.14'), + ('libjpeg-turbo', '1.4.0'), + ('FFTW', '3.3.4'), + ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb similarity index 64% rename from easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index 0f9bc0fa5f..82d76eef0e 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -9,17 +9,24 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'intel', 'version': '2015a'} -patches = ['sqlite_imports.patch', 'library_imports.patch'] +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver dependencies = [ ('Java', '1.8.0_40', '', True), - ('Python', '2.7.9'), # should have a working sqlite, and provide numpy - ('freetype', '2.5.5'), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/library_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/library_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch new file mode 100644 index 0000000000..c79477e52b --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch @@ -0,0 +1,13 @@ +--- install.sh.orig 2014-04-03 10:46:46.000000000 +0300 ++++ install.sh 2015-06-17 10:09:32.000000000 +0300 +@@ -820,8 +820,8 @@ + DO_PYTHON=1 + DO_PYMOD=1 + elif [ "${WITH_PYTHON}" = "false" ]; then +- DO_PYTHON=1 +- DO_PYMOD=1 ++ DO_PYTHON=0 ++ DO_PYMOD=0 + else + echoRed "Parameter --python only accept true or false values. Ignored and assuming default value." + fi -- GitLab From 4f2f3dc7bd35b80c5dc8c4e8c6fa80f6c3470da0 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 15:21:02 +0200 Subject: [PATCH 0502/1172] add bzip2 and Tcl goolf-1.7.20 dependencies --- .../b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb | 15 +++++++++++ .../t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb | 25 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..ddcc6fecd4 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.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': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..41060701af --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.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': '1.7.20'} + +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 be641b171fb4b3262ed87bdf06dec77a8f96ca5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:22:32 +0200 Subject: [PATCH 0503/1172] {vis}[goolf/1.4.10] Xmipp 3.1 --- .../Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb new file mode 100644 index 0000000000..7318afff3e --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -0,0 +1,16 @@ +name = 'Xmipp' +version = '3.1' +versionsuffix = '-with-incl-deps' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# note: all other dependencies are taken care of by Xmipp itself +dependencies = [('Java', '1.8.0_40', '', True)] + +moduleclass = 'vis' -- GitLab From 184a2db03b94d8ba511a524269dff58c3acd5053 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 15:29:45 +0200 Subject: [PATCH 0504/1172] add dependencies libffi and gettext goolf-1.7.20 --- .../g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 18 +++++++++++++++ .../l/libffi/libffi-3.1-goolf-1.7.20.eb | 23 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..55016086e0 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +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': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..c0ec3f2067 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +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': 'goolf', 'version': '1.7.20'} + +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' -- GitLab From 5f300753aeee98712f01a55636d1d38d2629aff8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:29:55 +0200 Subject: [PATCH 0505/1172] add missing easyconfigs, fix FFTW dep in Xmipp easyconfig for foss/2015a --- .../h/HDF5/HDF5-1.8.14-foss-2015a.eb | 51 ++++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb | 60 +++++++++++++++++++ .../Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- 3 files changed, 112 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000..c3c747459d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_11-02-41 +name = 'HDF5' +version = "1.8.14" + +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': '2015a'} +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 = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.2.0dev", + "easybuild-easyblocks_version": "2.2.0dev", + "timestamp": 1434441761, + "build_time": 176.49, + "install_size": 31544778, + "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-software-version=1.8.14', 'HDF5-1.8.13-foss-2015a.eb'], + "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "taito-login4.csc.fi", + "os_name": "RHEL", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb new file mode 100644 index 0000000000..025b0d6e1a --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -0,0 +1,60 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +# misleading name, this is a 'stable' release +version = '4.0.4beta' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.2.0dev", + "easybuild-easyblocks_version": "2.2.0dev", + "timestamp": 1434441102, + "build_time": 62.66, + "install_size": 4614536, + "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-toolchain="[\'foss\', \'2015a\']"', 'Xmipp-3.1-intel-2015a.eb'], + "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "taito-login4.csc.fi", + "os_name": "RHEL", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 3d82992342..fc928c6c57 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), - ('FFTW', '3.3.4'), + ('FFTW', '3.3.4', '', ('gompi', '2015a')), ('SQLite', '3.8.8.1'), # must match SQLite used by Python ('matplotlib', '1.4.3', versionsuffix), ] -- GitLab From 160836570895f4931dd6a62e25b6038c3717d599 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 15:48:10 +0200 Subject: [PATCH 0506/1172] Cosmetics and added checksums --- .../c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb | 17 ++++++++++---- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 19 +++++++++++---- .../c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 8 +++++-- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 23 +++++++++++-------- .../c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 17 ++++++++++---- 5 files changed, 58 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index b1b5830754..94eaf15f8d 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'ConfigureMake' name = "Cube" @@ -20,9 +24,12 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist/cube-3.4.3.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '703d4681851a5abf50946868f05e8f9e', # cube-3.4.3.tar.gz +] dependencies = [('Qt', '4.8.4')] diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index 941a048ad1..7159c84d00 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -30,16 +33,22 @@ patches = [ 'Cube-4.2_fix-with-qt-check.patch', ] +checksums = [ + 'aa1b1594bacddd3a1931f9a9dea23ce8', # cube-4.2.tar.gz + 'da69fe49d347dc7722c30bb785106d96', # Cube-4.2_fix-Qt-version-check.patch + '5a746d4f6f4eb5eb8b464ca355b46891', # Cube-4.2_fix-with-qt-check.patch +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index b4f0251684..7bda257ed2 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -21,16 +21,20 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +checksums = [ + '8f95b9531f5a8f8134f279c2767c9b20', # cube-4.2.3.tar.gz +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index c0a4d9c729..01eebc5f7e 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -29,14 +33,15 @@ checksums = [ dependencies = [('Qt', '4.8.6')] +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } -# If all prerequisites for the Cube Java reader are available on the system, -# parallel builds will fail. Alternatively, disable the Java reader using -# configopts = "--without-java-reader" -maxparallel = 1 - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb index 0a2aec777e..560d4ea5c5 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -24,16 +27,20 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } -- GitLab From 639239fcb05b2a8116b2371cde76a3713bcf5f55 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 15:48:28 +0200 Subject: [PATCH 0507/1172] Add easyconfig for latest release which no longer includes Java reader --- .../c/Cube/Cube-4.3.2-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000..b12da485bc --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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 = "4.3.2" + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'a9119524df5a39e7a5bf6dee4de62e30', # cube-4.3.2.tar.gz +] + +dependencies = [('Qt', '4.8.6')] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From 5bcead1e283193bdd88aacbee2ec931ea0d0a708 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:11:50 +0200 Subject: [PATCH 0508/1172] leading space --- .../easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb index 55016086e0..b9b28dda44 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -5,8 +5,8 @@ version = '0.19.2' 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""" + build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools + and documentation""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From 31abb3bac4d92482ed63daf9f0286a9a4997314b Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:12:35 +0200 Subject: [PATCH 0509/1172] leading space --- easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb index c0ec3f2067..bb8ee020a7 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -4,8 +4,8 @@ name = 'libffi' version = '3.1' 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.""" + 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': 'goolf', 'version': '1.7.20'} -- GitLab From f61c083dc61b1843d20c4677f34cb3d86e11ede5 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:14:49 +0200 Subject: [PATCH 0510/1172] leading space, align with common dependencies --- .../easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb index e57987a01a..3638dbedbc 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -5,8 +5,8 @@ version = '1.12.18' 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""" + 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': 'goolf', 'version': '1.7.20'} @@ -14,13 +14,13 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ('libpng', '1.6.12'), ('freetype', '2.5.3'), - ('zlib', '1.2.8'), ('pixman', '0.32.6'), ('fontconfig', '2.11.1'), ('expat', '2.1.0'), - ('bzip2', '1.0.6'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -- GitLab From 342522aa9b885b60dab7b449103d9be1f9ab6d04 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:16:40 +0200 Subject: [PATCH 0511/1172] align with common dependencies --- .../g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 85c9d54c28..0139533b6f 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -14,15 +14,15 @@ source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.12'), ('freetype', '2.5.3'), ('fontconfig', '2.11.1'), ('GLib', '2.40.0'), ('libjpeg-turbo', '1.3.1'), - ('libpng', '1.6.12'), ('expat', '2.1.0'), ('cairo', '1.12.18'), ('LibTIFF', '4.0.3'), - ('zlib', '1.2.8'), ] configopts = "--with-system-libtiff --enable-dynamic" -- GitLab From 9706a5ce64f82ffd5b6b230d92de392eaecaf2a6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:22:54 +0200 Subject: [PATCH 0512/1172] libpng to version 1.6.17 --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 0139533b6f..c8c894d270 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('zlib', '1.2.8'), - ('libpng', '1.6.12'), + ('libpng', '1.6.17'), ('freetype', '2.5.3'), ('fontconfig', '2.11.1'), ('GLib', '2.40.0'), -- GitLab From 9ddfed122fd50b3d218baaef796138b344a25675 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:26:25 +0200 Subject: [PATCH 0513/1172] fix wrong indent --- easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb index bb8ee020a7..ba1db82dae 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'libffi' version = '3.1' homepage = 'http://sourceware.org/libffi/' - description = """The libffi library provides a portable, high level programming interface to various calling +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': 'goolf', 'version': '1.7.20'} -- GitLab From 4d3f6a654ee0dce273372760bbf13e948194f2d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 08:50:15 +0200 Subject: [PATCH 0514/1172] bump versions: OpenMPI 1.8.6 + hwloc 1.11.0 --- easybuild/easyconfigs/g/gompi/gompi-2015b.eb | 2 +- ....10.1-GNU-5.1.0-2.25.eb => hwloc-1.11.0-GNU-5.1.0-2.25.eb} | 2 +- ....8.5-GNU-5.1.0-2.25.eb => OpenMPI-1.8.6-GNU-5.1.0-2.25.eb} | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.10.1-GNU-5.1.0-2.25.eb => hwloc-1.11.0-GNU-5.1.0-2.25.eb} (98%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-1.8.5-GNU-5.1.0-2.25.eb => OpenMPI-1.8.6-GNU-5.1.0-2.25.eb} (96%) diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb index a915cf4f95..0679b7fad6 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -17,7 +17,7 @@ tcver = '%s-binutils-%s' % (gccver, binutilsver) dependencies = [ ('GCC', gccver, '-binutils-%s' % binutilsver), ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + ('OpenMPI', '1.8.6', '', ('GNU', '%s-%s' % (gccver, binutilsver))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb similarity index 98% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb index c8e52b3fe3..71b80ef6aa 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' -version = '1.10.1' +version = '1.11.0' homepage = 'http://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb index 5973ddafd1..2181534b7c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = '1.8.5' +version = '1.8.6' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -dependencies = [('hwloc', '1.10.1')] +dependencies = [('hwloc', '1.11.0')] 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 -- GitLab From 420e2645b16ba64772da1b2a8b341a068546780b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 08:51:03 +0200 Subject: [PATCH 0515/1172] bump to OpenMPI1.8.6 --- easybuild/easyconfigs/f/foss/foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb index 415cfd1a90..2bb9b25e02 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -30,7 +30,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) dependencies = [ ('GCC', gccver, '-binutils-%s' % binutilsver), ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + ('OpenMPI', '1.8.6', '', ('GNU', '%s-%s' % (gccver, binutilsver))), (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From e5f696794565f468ed58d137e93e81c73b54ca32 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Thu, 18 Jun 2015 09:11:11 +0200 Subject: [PATCH 0516/1172] leading space, dependencies moved below sources --- easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb index 72296e698f..eb194cd37c 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -5,7 +5,7 @@ version = '3.6' homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -13,11 +13,11 @@ java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] - source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] +dependencies = [(java, javaver)] + checksums = ['f4571413833df913261ff76b6f40bb76'] sanity_check_paths = { -- GitLab From 32292e9427b0030b3c9403bd03314e16faca83b2 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Thu, 18 Jun 2015 09:11:34 +0200 Subject: [PATCH 0517/1172] lead --- easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb index 7e0c5d595f..8b1570a181 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -5,7 +5,7 @@ version = '4.1d' homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -13,11 +13,11 @@ java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] - source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] +dependencies = [(java, javaver)] + checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] sanity_check_paths = { -- GitLab From 56cf9da32ad909f325a150a28facfe0a2f820f6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 10:14:38 +0200 Subject: [PATCH 0518/1172] fix PyPI URLs: use https --- .../Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015.05.eb | 12 ++++++------ .../Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 08f3c850f6..5b829d6a73 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.22' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index e5b95d6f14..3290f94dba 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - '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')], @@ -46,13 +46,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + '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/'], diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb index 28482a1b30..335241b807 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb index e95fac6936..a9aa394aab 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,7 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 7b78b8c68555e2713d89479e296699758f97c03a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 11:20:29 +0200 Subject: [PATCH 0519/1172] {vis}[foss/2015a] SPIDER 22.10 --- .../s/SPIDER/SPIDER-22.10-foss-2015a.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10_gfortran49.patch | 22 ++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb new file mode 100644 index 0000000000..31a4eb409a --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = [ + 'SPIDER-%(version)s_fix-syntax-ifort.patch', + 'SPIDER-%(version)s_gfortran49.patch', +] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_GFORTRAN -cpp -dM -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch new file mode 100644 index 0000000000..3ffd041738 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch @@ -0,0 +1,22 @@ +--- spider/src/copy1.f.orig 2015-06-16 18:11:37.000000000 +0300 ++++ spider/src/copy1.f 2015-06-16 18:12:12.000000000 +0300 +@@ -72,6 +72,8 @@ + INTEGER, PARAMETER :: LUNXM1 = 83 + INTEGER, PARAMETER :: LUNXM2 = 84 + ++ LOGICAL :: VERBOSET ++ + C FROM/'AS','MR','PD','RA','NI','TE','VA','EM','NT','XP'/ + + C TO/'AS','BR','MR','PO','RA','TI','XP','OP','JPG'/ +--- spider/src/pr3d.f.orig 2015-06-16 18:49:45.000000000 +0300 ++++ spider/src/pr3d.f 2015-06-16 18:50:05.000000000 +0300 +@@ -75,7 +75,7 @@ + + CALL SET_MPI(ICOMM,MYPID,MPIERR) + +- WANTSQRTS = (FSCOP == .TRUE.) ++ WANTSQRTS = (FSCOP .eqv. .TRUE.) + + C INPUT FIRST IMAGE + MAXIM = 0 -- GitLab From 1c5365d353a6ec6f3243cd9edad6f819816f1d5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 11:42:08 +0200 Subject: [PATCH 0520/1172] use Java 1.7 as dep in Xmipp 3.1 easyconfig --- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 7318afff3e..c1f4fa485c 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -11,6 +11,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.8.0_40', '', True)] +dependencies = [('Java', '1.7.0_80', '', True)] moduleclass = 'vis' -- GitLab From 84842c86f6c7892fb05912715197176fcd38f933 Mon Sep 17 00:00:00 2001 From: npklein Date: Thu, 18 Jun 2015 15:51:30 +0200 Subject: [PATCH 0521/1172] readd .eb file after accidentally syncing it out --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..2eabb347c9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://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 = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://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'), + #('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': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + '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': ['https://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': ['https://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' -- GitLab From a24cf6c099160dfc700f1e35cb9ca10d10e15e84 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 19 Jun 2015 10:37:00 +0200 Subject: [PATCH 0522/1172] Add Tk --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 2eabb347c9..c011298dc9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -20,6 +20,7 @@ dependencies = [ ('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 ] -- GitLab From 2f000ca752464e850fc7e35985cf06edc4e5cede Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 19 Jun 2015 10:53:15 +0200 Subject: [PATCH 0523/1172] add dependency Tk-8.6.3-goolf-1.7.20-no0X11 --- .../t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb 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 new file mode 100644 index 0000000000..025f5e6476 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +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': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 35e15ed2fec6006e9eaa57d3e76c0c70dadd4492 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 14:06:30 +0200 Subject: [PATCH 0525/1172] {lang}[foss/2015b] Python 2.7.10 --- .../b/bzip2/bzip2-1.0.6-foss-2015b.eb | 15 +++ .../libreadline/libreadline-6.3-foss-2015b.eb | 27 ++++ .../n/ncurses/ncurses-5.9-foss-2015b.eb | 18 +++ .../p/Python/Python-2.7.10-foss-2015b.eb | 121 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-foss-2015b.eb | 38 ++++++ .../easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb | 25 ++++ .../t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb | 24 ++++ .../z/zlib/zlib-1.2.8-foss-2015b.eb | 22 ++++ 8 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb new file mode 100644 index 0000000000..1e97fbfcef --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.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': 'foss', 'version': '2015b'} +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-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb new file mode 100644 index 0000000000..1c079c55a6 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -0,0 +1,27 @@ +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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-foss-2015b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.eb new file mode 100644 index 0000000000..fd95bcc678 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.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': 'foss', 'version': '2015b'} +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/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb new file mode 100644 index 0000000000..8d705315cc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -0,0 +1,121 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb new file mode 100644 index 0000000000..15e2ab0e51 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015b'} + +# 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', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb new file mode 100644 index 0000000000..ba9826c847 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.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': 'foss', 'version': '2015b'} + +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-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb new file mode 100644 index 0000000000..a7e3e3028a --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-foss-2015b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.eb new file mode 100644 index 0000000000..e39bc78804 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.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': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 9e0ef7975cb5955c5720eca2c75e87221035e13b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 14:07:31 +0200 Subject: [PATCH 0526/1172] {lang}[intel/2015b] Python 2.7.10 --- .../b/bzip2/bzip2-1.0.6-intel-2015b.eb | 15 +++ .../libreadline-6.3-intel-2015b.eb | 27 ++++ .../n/ncurses/ncurses-5.9-intel-2015b.eb | 18 +++ .../p/Python/Python-2.7.10-intel-2015b.eb | 121 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-intel-2015b.eb | 38 ++++++ .../t/Tcl/Tcl-8.6.4-intel-2015b.eb | 25 ++++ .../t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb | 24 ++++ .../z/zlib/zlib-1.2.8-intel-2015b.eb | 22 ++++ 8 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb new file mode 100644 index 0000000000..b45764711d --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.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': '2015b'} +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-intel-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb new file mode 100644 index 0000000000..de61e222ce --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -0,0 +1,27 @@ +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': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-intel-2015b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.eb new file mode 100644 index 0000000000..7a48798be8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.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': '2015b'} +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/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb new file mode 100644 index 0000000000..a5115dc2be --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -0,0 +1,121 @@ +name = 'Python' +version = '2.7.10' + +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': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb new file mode 100644 index 0000000000..f343fd6993 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015b'} + +# 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', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb new file mode 100644 index 0000000000..ae2268790f --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.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': '2015b'} + +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-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb new file mode 100644 index 0000000000..2a26e9ef0a --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -0,0 +1,24 @@ +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': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +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-2015b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.eb new file mode 100644 index 0000000000..a09231ac58 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.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': '2015b'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From a56d4d1df292ecd07c03b0504821a7da1ab1f80d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 14:13:53 +0200 Subject: [PATCH 0527/1172] fix style remark --- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb index 2181534b7c..c54ad5d8b7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } -- GitLab From f36930c01c30076a5db2d9307ef4c789f4958d43 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 22 Jun 2015 14:43:19 +0200 Subject: [PATCH 0528/1172] added checksum --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index c8c894d270..bcdc3829f0 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] +checksums ['818c87e31f7562aaa97397d3d0cc20a1'] + dependencies = [ ('zlib', '1.2.8'), ('libpng', '1.6.17'), -- GitLab From 12665fcfb1fadd6e78edb38490f9b54676380d00 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 22 Jun 2015 14:57:13 +0200 Subject: [PATCH 0529/1172] add forgotten '=' with checksums --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index bcdc3829f0..e1f6e215e7 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] -checksums ['818c87e31f7562aaa97397d3d0cc20a1'] +checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] dependencies = [ ('zlib', '1.2.8'), -- GitLab From ff2d728913db076780847346429d6e6adecd78e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 15:29:07 +0200 Subject: [PATCH 0530/1172] {tools}[foss+intel/2015a] bibtexparser 0.5 + 0.6.0 --- ...ibtexparser-0.5-foss-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...btexparser-0.5-intel-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...texparser-0.6.0-foss-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...exparser-0.6.0-intel-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ 4 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..383c7de16a --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4c591a3fc0 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7060a6e07d --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..88ee53e88a --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' -- GitLab From 954a0f35479621559df7fad840139540fa832e96 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 22 Jun 2015 15:29:13 +0200 Subject: [PATCH 0531/1172] add dependency for libpng-1.6.17 --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 270e7df776..c45c55b783 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -17,6 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] # these are actually patched and included in the sources, dependencies = [ ('LibTIFF', '4.0.3'), + ('libpng', '1.6.17'), ] configopts = "--with-system-libtiff --enable-dynamic" -- GitLab From a300b1676b6664806c012d561ab9df20cc629318 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 22 Jun 2015 15:45:39 +0200 Subject: [PATCH 0532/1172] remove double libpng dependency --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 052e198375..e1f6e215e7 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -25,7 +25,6 @@ dependencies = [ ('expat', '2.1.0'), ('cairo', '1.12.18'), ('LibTIFF', '4.0.3'), - ('libpng', '1.6.17'), ] configopts = "--with-system-libtiff --enable-dynamic" -- GitLab From 4917b5409021d8750177ef477da4dd4a76d460db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 15:51:12 +0200 Subject: [PATCH 0533/1172] style fix in OpenMPI easyconfigs --- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 5 ++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 5 ++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 5 ++--- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 9 +++------ .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 9 ++++----- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 7 ++++--- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 9 +++------ .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 10 +++------- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 9 +++------ .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 6 ++---- 29 files changed, 75 insertions(+), 122 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index e568f8411e..e2dcab157e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -17,11 +17,10 @@ patches = ['pax_disable.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] 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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index fe72e01efd..af837e0815 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -17,11 +17,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] 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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index a53d8baacf..c95534677f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -26,11 +26,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] 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 ["mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7..6c869405ae 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721..9efd057826 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55..5eadff7219 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945..6d4df930a7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,15 +19,14 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77" ,"mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0..653bf81122 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7..9a90f6103b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,12 +24,13 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e3449..72d77b0d4b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -18,12 +18,11 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda8..a762cb5756 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -18,12 +18,11 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617..2e51419ed1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -20,12 +20,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d..380ed604f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -21,12 +21,11 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfa..16d67f2c01 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -23,12 +23,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613df..6efbf16c1c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -23,12 +23,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f..219134b916 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271..4c2e264500 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,18 +18,14 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d..a29d619ce5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b..6687a0ffa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,12 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index fdf4f47fc8..3e20609bc6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -31,12 +31,10 @@ configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --d # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720..eeb7c2fe82 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd41..a47fa4f0f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2..c6c6f0c9ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,12 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c..39b44f0df0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.9')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2..2eb439ac34 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3b..e009a63259 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f..780c3c78ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6..ca0afea9dc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,12 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 17455567fb..095d22d991 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } -- GitLab From 81d0916a9bd0bf6ee4927db62532556a7667ac08 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 22 Jun 2015 16:03:53 +0200 Subject: [PATCH 0534/1172] use libpng 1.6.12 --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index e1f6e215e7..66e39de29b 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -17,7 +17,7 @@ checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] dependencies = [ ('zlib', '1.2.8'), - ('libpng', '1.6.17'), + ('libpng', '1.6.12'), ('freetype', '2.5.3'), ('fontconfig', '2.11.1'), ('GLib', '2.40.0'), -- GitLab From 5a802805e9a499b8fd1b054a6957581d2ba0cc8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 16:07:40 +0200 Subject: [PATCH 0535/1172] fix syntax issues --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 2 +- 15 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 6c869405ae..d88a606fa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 9efd057826..63ad283770 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 5eadff7219..6562c8883f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 6d4df930a7..0d984429f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -23,7 +23,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 653bf81122..1c96459eb6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 9a90f6103b..825a5a7a0c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -28,7 +28,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 72d77b0d4b..2501ef80eb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index a762cb5756..a58e7c5d7e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 2e51419ed1..c542435f08 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 380ed604f3..4628f0030f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 16d67f2c01..8106b6d183 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -27,7 +27,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 6efbf16c1c..16eab6b12c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -27,7 +27,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 219134b916..33b34df331 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4c2e264500..19ad55fe18 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index a29d619ce5..9c2f4e66f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "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], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], -- GitLab From 15e3c190fe31987971b783e207dffe180aced312 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 16:59:59 +0200 Subject: [PATCH 0536/1172] remove buildstats that snuck in --- .../fontconfig-2.11.1-intel-2015a.eb | 2 +- .../h/HDF5/HDF5-1.8.14-foss-2015a.eb | 25 ------------------- .../l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb | 25 ------------------- 3 files changed, 1 insertion(+), 51 deletions(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb index a8f2612b6a..54455c5111 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.5.5'), + ('freetype', '2.5.5'), ] configopts = '--disable-docs ' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb index c3c747459d..35077bfe35 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -24,28 +24,3 @@ dependencies = [ ] moduleclass = 'data' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.2.0dev", - "easybuild-easyblocks_version": "2.2.0dev", - "timestamp": 1434441761, - "build_time": 176.49, - "install_size": 31544778, - "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-software-version=1.8.14', 'HDF5-1.8.13-foss-2015a.eb'], - "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "taito-login4.csc.fi", - "os_name": "RHEL", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb index 025b0d6e1a..accbb2bb0a 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -33,28 +33,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.2.0dev", - "easybuild-easyblocks_version": "2.2.0dev", - "timestamp": 1434441102, - "build_time": 62.66, - "install_size": 4614536, - "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-toolchain="[\'foss\', \'2015a\']"', 'Xmipp-3.1-intel-2015a.eb'], - "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/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=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "taito-login4.csc.fi", - "os_name": "RHEL", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From a52548e1f0a804fa6339ede3b322fb7ffd3997e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:44:44 +0200 Subject: [PATCH 0537/1172] {tools}[intel/2015a] IPython 3.2.3 --- .../IPython-3.1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../IPython-3.2.3-intel-2015a-Python-2.7.9.eb | 42 +++++++++++++++++++ ...MQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb | 33 +++++++++++++++ ...requests-2.7.0-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++ 4 files changed, 105 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index 377e678904..f7ad35c7e1 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -18,7 +18,7 @@ source_urls = ['http://archive.ipython.org/release/%(version)s/'] python = 'Python' pyver = '2.7.9' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..e3beaf3595 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,42 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.3' + +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'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..0986a01c06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-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': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +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/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f8a41a318c --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' -- GitLab From 662bee79fd88155cfe1b48fd9a54c9a901bd7e85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:46:30 +0200 Subject: [PATCH 0538/1172] {tools}[foss/2015a] IPython 3.2.3 --- ...IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../IPython-3.2.3-foss-2015a-Python-2.7.9.eb | 42 +++++++++++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb | 27 ++++++++++++ ...ZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb | 33 +++++++++++++++ .../Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 29 +++++++++++++ .../pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb | 32 ++++++++++++++ .../requests-2.7.0-foss-2015a-Python-2.7.9.eb | 29 +++++++++++++ .../util-linux-2.26.1-foss-2015a.eb | 33 +++++++++++++++ .../z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb | 34 +++++++++++++++ 9 files changed, 260 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 3c52ea836c..be492fa165 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://archive.ipython.org/release/%(version)s/'] python = 'Python' pyver = '2.7.3' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..96b5821500 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,42 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.3' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb new file mode 100644 index 0000000000..6dae1dce85 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.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': '2015a'} + +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-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..fca9d5270f --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-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': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +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/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 new file mode 100644 index 0000000000..103bb38998 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..27ca7fc128 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..d4e3a34ddb --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb new file mode 100644 index 0000000000..dc874b1a62 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.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': 'foss', 'version': '2015a'} + +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-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb new file mode 100644 index 0000000000..537ac748fe --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.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': 'foss', 'version': '2015a'} + +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.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 49bb0438d2fcd6a5192c3440dc1ea693d540bf28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:48:04 +0200 Subject: [PATCH 0539/1172] {devel}[*/2015a] Boost 1.5.8.0 w/ Python 2.7.10 --- .../Boost-1.58.0-foss-2015a-Python-2.7.10.eb | 25 +++++++++++++++++++ .../Boost-1.58.0-intel-2015a-Python-2.7.10.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..76622b0263 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +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} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..d48f0872dd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 1c0d6839ddd3a32938ffa015eb61737275576c70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:48:37 +0200 Subject: [PATCH 0540/1172] {data}[*/2015a] HDF5 1.8.15-patch1 --- .../h/HDF5/HDF5-1.8.15-foss-2015a.eb | 23 ++++++++++++++++ .../h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb | 23 ++++++++++++++++ .../h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb | 26 +++++++++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb new file mode 100644 index 0000000000..ef7549e987 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15' + +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': '2015a'} +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 = ['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/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb new file mode 100644 index 0000000000..a9ec210198 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -0,0 +1,23 @@ +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': 'foss', 'version': '2015a'} +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 = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb new file mode 100644 index 0000000000..ec9b5d3a8a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 0c9dd9122eaf8be350cbe5d5a11b4234c41fe608 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 22 Jun 2015 17:55:18 +0200 Subject: [PATCH 0541/1172] update dependencies to new version --- .../c/cairo/cairo-1.14.2-goolf-1.7.20.eb | 29 +++++++++++++++++++ .../fontconfig-2.11.94-goolf-1.7.20.eb | 22 ++++++++++++++ .../f/freetype/freetype-2.6-goolf-1.7.20.eb | 21 ++++++++++++++ .../g/GLib/GLib-2.45.2-goolf-1.7.20.eb | 21 ++++++++++++++ .../Ghostscript-9.16-goolf-1.7.20.eb | 14 ++++----- .../l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb | 22 ++++++++++++++ .../libjpeg-turbo-1.4.1-goolf-1.7.20.eb | 24 +++++++++++++++ 7 files changed, 146 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..63d09e359a --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.2' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('pixman', '0.32.6'), + ('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-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb new file mode 100644 index 0000000000..8fdfa9a81b --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.6'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..484ef7705a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +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/g/GLib/GLib-2.45.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..34fcc7fc85 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.45.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 66e39de29b..646b1a796e 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -17,14 +17,14 @@ checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] dependencies = [ ('zlib', '1.2.8'), - ('libpng', '1.6.12'), - ('freetype', '2.5.3'), - ('fontconfig', '2.11.1'), - ('GLib', '2.40.0'), - ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.16'), + ('freetype', '2.6.0'), + ('fontconfig', '2.11.94'), + ('GLib', '2.45.2'), + ('libjpeg-turbo', '1.4.1'), ('expat', '2.1.0'), - ('cairo', '1.12.18'), - ('LibTIFF', '4.0.3'), + ('cairo', '1.14.2'), + ('LibTIFF', '4.0.4'), ] configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..8858538d5a --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..af63e0180b --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +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': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' -- GitLab From 3eeeedb83b6aac99d2a1bff51947fd861ba32218 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 22 Jun 2015 17:59:18 +0200 Subject: [PATCH 0542/1172] libpng 1.6.17 instead of 1.6.16 --- .../g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 646b1a796e..6f0a08c361 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -17,8 +17,8 @@ checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] dependencies = [ ('zlib', '1.2.8'), - ('libpng', '1.6.16'), - ('freetype', '2.6.0'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('GLib', '2.45.2'), ('libjpeg-turbo', '1.4.1'), -- GitLab From 8cb2351f31b92d82dce6580016c863c09cb33fbc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 18:16:51 +0200 Subject: [PATCH 0543/1172] fix change in sanity check paths for OpenMPI 1.6.4 and 1.6.5 --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ++-- .../OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ++-- 14 files changed, 28 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 63ad283770..b42d9a8b03 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 6562c8883f..fc479108fe 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 0d984429f3..8b588833b0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,8 +19,8 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 1c96459eb6..168f6f9d23 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 825a5a7a0c..933369e32b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,8 +24,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 2501ef80eb..7c0a81dc4a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -18,8 +18,8 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index a58e7c5d7e..125d5b989d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -18,8 +18,8 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index c542435f08..aaa6f69c8d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -20,8 +20,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 4628f0030f..fcb341d4f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -21,8 +21,8 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 8106b6d183..c3cb7f8713 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -23,8 +23,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 16eab6b12c..125577dc71 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -23,8 +23,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 33b34df331..4fc8978e4d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,8 +20,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 19ad55fe18..0bb4349893 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,8 +18,8 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 9c2f4e66f1..e9f2f244ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,8 +20,8 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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] + -- GitLab From 0cb03e18fbd1985cb0b72dba6a485a12878fba11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 18:43:23 +0200 Subject: [PATCH 0544/1172] {vis}[*/2015a] PyQt 4.11.4 --- .../PyQt-4.11.4-foss-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ .../PyQt-4.11.4-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ .../SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++ .../SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++ 4 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..34baa22804 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..789bf13b2c --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..e745733edd --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..87b18fbf3c --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' -- GitLab From 8fdf2e62a4bbed665e4d9df06c77b939548aba04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 20:14:48 +0200 Subject: [PATCH 0545/1172] correct IPython version to 3.2.0 --- ...Python-2.7.9.eb => IPython-3.2.0-foss-2015a-Python-2.7.9.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.2.3-foss-2015a-Python-2.7.9.eb => IPython-3.2.0-foss-2015a-Python-2.7.9.eb} (98%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb index 96b5821500..c15643b57e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.2.3' +version = '3.2.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: -- GitLab From 2beb46eb0f0fa694489751f090d4299c95ec6090 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 20:15:34 +0200 Subject: [PATCH 0546/1172] correct IPython version to 3.2.0 --- ...ython-2.7.9.eb => IPython-3.2.0-intel-2015a-Python-2.7.9.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.2.3-intel-2015a-Python-2.7.9.eb => IPython-3.2.0-intel-2015a-Python-2.7.9.eb} (98%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb index e3beaf3595..5494f4a74f 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.2.3' +version = '3.2.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: -- GitLab From 6539abef5d240218e11f6102b69699fa837e9b49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:38:46 +0200 Subject: [PATCH 0547/1172] add PyPI source URL for IPython --- .../i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb index 5494f4a74f..5b0893e10b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From a79e01150c3db6ca87c8d5e13ca1edbaeb6a1987 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:39:40 +0200 Subject: [PATCH 0548/1172] add PyPI source URL for IPython --- .../i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 5 ++++- .../i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index be492fa165..92f605169b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb index c15643b57e..ca831cfe27 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From 0ff8e2b924ff001f2a4a83b622caa3cba84e260f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:40:33 +0200 Subject: [PATCH 0549/1172] add PyPI source URL for IPython 3.1.0 --- .../i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index f7ad35c7e1..4ddce0d142 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From 9f197374adf6f9fa897b2f2660fa2150b3da80a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:45:08 +0200 Subject: [PATCH 0550/1172] add patch for Qt 4.8.6 with intel/2015a --- .../easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb | 5 ++++- .../easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch | 15 +++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index 7ca9946d90..1ab132124a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -12,7 +12,10 @@ source_urls = [ ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -patches = ['Qt-4.8.6_icc-qUnused.patch'] +patches = [ + 'Qt-%(version)s_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] dependencies = [('GLib', '2.40.0')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch new file mode 100644 index 0000000000..4170411ac1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch @@ -0,0 +1,15 @@ +fixed for error "undefined reference to `vtable for Phonon::ObjectDescriptionModel<(Phonon::ObjectDescriptionType)0>'" +that occurs (only) on some systems (e.g. RHEL6/Sandy Bridge) +based on https://forum.qt.io/topic/35044/build-failure-4-8-5-on-mac-with-phonon/9 +author: Kenneth Hoste (HPC-UGent) +--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h.orig 2015-06-22 23:18:54.723573581 +0300 ++++ qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h 2015-06-22 23:19:16.902399019 +0300 +@@ -141,7 +141,7 @@ + + /* Required to ensure template class vtables are exported on both symbian + and existing builds. */ +-#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) ++#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) || defined(Q_CC_INTEL) + // RVCT compiler (2.2.686) requires the export declaration to be on the class to export vtables + // MWC compiler works both ways + // GCCE compiler is unknown (it can't compile QtCore yet) -- GitLab From c1d5caa98cdce1a88eb94ca8058978bd285ef085 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 11:15:41 +0200 Subject: [PATCH 0551/1172] add M4 as build dep for GCC 5.1.0 --- .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 5 +++- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 27 +++++++++++++++++++ 3 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index b9370c56ff..44330ce226 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -29,7 +29,10 @@ sources = [ 'isl-0.14.tar.bz2', ] -builddependencies = [('binutils', binutilsver)] +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', binutilsver), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 4968008ae8..9097cd1a47 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -28,6 +28,8 @@ sources = [ patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +builddependencies = [('M4', '1.4.17')] + checksums = [ 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb new file mode 100644 index 0000000000..9c1b1f5017 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -0,0 +1,27 @@ +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': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 3531d75cc20918188a3f98e6cc268f48f0c75a74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 11:26:37 +0200 Subject: [PATCH 0552/1172] remove unrequired patch in M4 1.4.17 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 9c1b1f5017..e76d5efa3d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,8 +15,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['M4-%(version)s-no-gets.patch'] - configopts = "--enable-cxx" sanity_check_paths = { -- GitLab From f6d70f78a16b69afb8a3c90c3107cd75458bbaa3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 12:42:00 +0200 Subject: [PATCH 0553/1172] use empty version in dummy toolchain so dependencies get loaded --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 44330ce226..8bbf0ea88e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -8,7 +8,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 9097cd1a47..a69c58da2c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -5,7 +5,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -- GitLab From 018f2c314563b66bb6dd770f097586ef87585595 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 13:28:11 +0200 Subject: [PATCH 0554/1172] {devel}[*/2015a] CMake 3.2.3 --- .../c/CMake/CMake-3.2.3-foss-2015a.eb | 22 +++++++++++++++++++ .../c/CMake/CMake-3.2.3-intel-2015a.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000..c7935c7c64 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -0,0 +1,22 @@ +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': 'foss', 'version': '2015a'} + +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' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb new file mode 100644 index 0000000000..f4cde92c3c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -0,0 +1,22 @@ +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': 'intel', 'version': '2015a'} + +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' -- GitLab From 18d49280a7c6b6ba740bbea1e9a4db57af06bac3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 13:56:59 +0200 Subject: [PATCH 0555/1172] style fix --- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index e76d5efa3d..3f396ce26b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -5,9 +5,9 @@ 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. + 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': 'dummy', 'version': 'dummy'} -- GitLab From be2c6392f6a001b60a64c909afba2eefc2de7c88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 15:04:54 +0200 Subject: [PATCH 0556/1172] {vis}[*/2015a] freetype 2.6 --- .../f/freetype/freetype-2.6-foss-2015a.eb | 21 +++++++++++++++++++ .../f/freetype/freetype-2.6-intel-2015a.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb new file mode 100644 index 0000000000..3678616622 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +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/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb new file mode 100644 index 0000000000..6a1b7e739c --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From 9721e2746dab0690179a0a14cab34631fde54a5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 15:51:29 +0200 Subject: [PATCH 0557/1172] {bio}[*/2015a] EMAN 2.11 --- .../EMAN2-2.11-foss-2015a-Python-2.7.9.eb | 44 +++++++++++++++++++ .../EMAN2-2.11-intel-2015a-Python-2.7.9.eb | 44 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb | 34 ++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb | 34 ++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f239ad58fc --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + # FFTW provided via toolchain + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b7a9c16a5a --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('FFTW', '3.3.4'), + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb new file mode 100644 index 0000000000..70578c5f23 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2015a'} + +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/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb new file mode 100644 index 0000000000..6b0d237d17 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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' -- GitLab From 4d840ee3d2aa6da3649c03dfbfac2db32e2ae22d Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Tue, 23 Jun 2015 16:06:14 +0200 Subject: [PATCH 0558/1172] fix wrong checksum --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 6f0a08c361..8c1bed1bc5 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] -checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] +checksums = ['829319325bbdb83f5c81379a8f86f38f'] dependencies = [ ('zlib', '1.2.8'), -- GitLab From a72d69bf1261c8bf409d5b9fa2d5f869640f35ab Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 23 Jun 2015 21:34:43 +0200 Subject: [PATCH 0559/1172] remove libpng-turbo from dependency --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 6f0a08c361..dab4295dc2 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] -checksums = ['818c87e31f7562aaa97397d3d0cc20a1'] +checksums = ['829319325bbdb83f5c81379a8f86f38f'] dependencies = [ ('zlib', '1.2.8'), @@ -21,7 +21,6 @@ dependencies = [ ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('GLib', '2.45.2'), - ('libjpeg-turbo', '1.4.1'), ('expat', '2.1.0'), ('cairo', '1.14.2'), ('LibTIFF', '4.0.4'), -- GitLab From d32f0dd08d8da1db6105daf58212d8808bd03a4f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 24 Jun 2015 00:58:20 +0200 Subject: [PATCH 0560/1172] Check for MPI-specific driver during sanity check --- .../v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index b3fef1121f..b5fb8fcae1 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -34,7 +34,7 @@ checksums = [ install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { - 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.so"], 'dirs': [] } -- GitLab From bea11c8332da0e58365732cb95b808787bfda8d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jun 2015 09:07:16 +0200 Subject: [PATCH 0561/1172] reinclude libjpeg-turbo dependency in Ghostscript easyconfig --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index dab4295dc2..8c1bed1bc5 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -21,6 +21,7 @@ dependencies = [ ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('GLib', '2.45.2'), + ('libjpeg-turbo', '1.4.1'), ('expat', '2.1.0'), ('cairo', '1.14.2'), ('LibTIFF', '4.0.4'), -- GitLab From 8c8be4785f137a1641ed0ad79e2d79492c06c730 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jun 2015 11:24:24 +0200 Subject: [PATCH 0562/1172] use libjpeg-turbo 1.3.1 as dep in Ghostscript easyconfig, 1.4.x doesn't work --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index 8c1bed1bc5..d473187b62 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('GLib', '2.45.2'), - ('libjpeg-turbo', '1.4.1'), + ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work ('expat', '2.1.0'), ('cairo', '1.14.2'), ('LibTIFF', '4.0.4'), -- GitLab From e8350ce57e79a84d5d8474fb248c7bb2bd6a4ec1 Mon Sep 17 00:00:00 2001 From: umcg-mterpstra Date: Wed, 24 Jun 2015 16:19:20 +0200 Subject: [PATCH 0563/1172] created cramtools-v2.0-Java-1.7.0_80.eb --- .../cramtools/cramtools-v2.0-Java-1.7.0_80.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..aab392a85f --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +name = 'cramtools' +version = '2.0' + +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': 'dummy'} +easyblock = 'Tarball' + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/cramtools-2.0.jar""" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' -- GitLab From 708fe7a6d4cd91c21ff1f84eb1025bdfac09ea3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jun 2015 17:01:20 +0200 Subject: [PATCH 0564/1172] set parallel=1 in SQLite easyconfig + enhance sanity_check_paths --- .../easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb index f343fd6993..2008f892f3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb @@ -30,9 +30,11 @@ dependencies = [ ('Tcl', '8.6.4'), ] +parallel = 1 + sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 5c50cb9a7517ffacc0e0ecbdc3430a7635c842a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jun 2015 17:02:07 +0200 Subject: [PATCH 0565/1172] set parallel=1 in SQLite easyconfig + enhance sanity_check_paths --- .../easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb index 15e2ab0e51..f71908ec0b 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb @@ -30,9 +30,11 @@ dependencies = [ ('Tcl', '8.6.4'), ] +parallel = 1 + sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From dc88b5311cf335f8e4dec1cd7e963ba8d33711b6 Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 24 Jun 2015 17:14:23 +0200 Subject: [PATCH 0566/1172] Update cramtools-v2.0-Java-1.7.0_80.eb --- .../c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb index aab392a85f..19162420ed 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb @@ -1,17 +1,19 @@ +easyblock = 'Tarball' + name = 'cramtools' version = '2.0' 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.""" +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': 'dummy'} -easyblock = 'Tarball' -# download manually from http://www.broadinstitute.org/gatk/download sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] - java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -- GitLab From a0c410cbe64ba3f83295cc7b207d73f9e023f146 Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 24 Jun 2015 17:22:23 +0200 Subject: [PATCH 0567/1172] Rename cramtools-v2.0-Java-1.7.0_80.eb to cramtools-2.0-Java-1.7.0_80.eb --- ...tools-v2.0-Java-1.7.0_80.eb => cramtools-2.0-Java-1.7.0_80.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cramtools/{cramtools-v2.0-Java-1.7.0_80.eb => cramtools-2.0-Java-1.7.0_80.eb} (100%) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb similarity index 100% rename from easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb rename to easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb -- GitLab From 0c577d7bde6b4d557ced343a304501f98629982b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 09:10:10 +0200 Subject: [PATCH 0568/1172] trivial style fixes --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 8 ++++---- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb | 8 ++++---- .../v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 62ddb26846..44f692903f 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "Vampir" version = "8.4.1" @@ -27,6 +27,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { @@ -34,9 +37,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index 379ca0d9f4..5596a89f02 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "Vampir" version = "8.4.1" @@ -30,6 +30,9 @@ checksums = [ '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin ] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { @@ -37,9 +40,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index b5fb8fcae1..5b068e3cf7 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "VampirServer" version = "8.4.1" @@ -31,6 +31,9 @@ checksums = [ '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin ] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { @@ -38,9 +41,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } -- GitLab From e631c18eb914b13437300cd5eba32e982ec66dab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 10:53:30 +0200 Subject: [PATCH 0569/1172] {lang}[intel/2015b] R 3.1.3 + 3.2.0-bare --- .../libjpeg-turbo-1.4.0-intel-2015b.eb | 24 ++ .../l/libpng/libpng-1.6.16-intel-2015b.eb | 19 + .../l/libpng/libpng-1.6.17-intel-2015b.eb | 19 + .../n/NASM/NASM-2.11.06-intel-2015b.eb | 31 ++ .../easyconfigs/r/R/R-3.1.3-intel-2015b.eb | 391 ++++++++++++++++++ .../r/R/R-3.2.0-intel-2015b-bare.eb | 27 ++ 6 files changed, 511 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb new file mode 100644 index 0000000000..2bb0e8f9bc --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb new file mode 100644 index 0000000000..21ff2f7764 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.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': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb new file mode 100644 index 0000000000..4c66e1d224 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb new file mode 100644 index 0000000000..f174be96fd --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-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:: 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 = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +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/r/R/R-3.1.3-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb new file mode 100644 index 0000000000..d4fb7b27b9 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb @@ -0,0 +1,391 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '4.4', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.6-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + 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'0.4.650.1.1', ext_options), + ('plyr', '1.8.1', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-40', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-12', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('mgcv', '1.8-5', ext_options), + ('minqa', '1.2.4', ext_options), + ('nloptr', '1.0.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('lme4', '1.1-7', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('quantreg', '5.11', ext_options), + ('car', '2.0-25', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), + ('sp', '1.0-17', ext_options), + ('vcd', '1.3-2', ext_options), + 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'1.0.2', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb new file mode 100644 index 0000000000..f840c8adba --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From 03154eb0d6f5f68e53e116a9c6ee288d1a6ac423 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 10:57:19 +0200 Subject: [PATCH 0570/1172] {lang}[foss/2015b] R 3.1.3 + 3.2.0-bare --- .../libjpeg-turbo-1.4.0-foss-2015b.eb | 24 ++ .../l/libpng/libpng-1.6.16-foss-2015b.eb | 19 + .../l/libpng/libpng-1.6.17-foss-2015b.eb | 19 + .../n/NASM/NASM-2.11.06-foss-2015b.eb | 31 ++ .../easyconfigs/r/R/R-3.1.3-foss-2015b.eb | 392 ++++++++++++++++++ .../r/R/R-3.2.0-foss-2015b-bare.eb | 27 ++ 6 files changed, 512 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015b.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb new file mode 100644 index 0000000000..d0e4377e82 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb new file mode 100644 index 0000000000..7d2de2d1c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb new file mode 100644 index 0000000000..e421fa225d --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015b.eb new file mode 100644 index 0000000000..397b3d64f4 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-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:: 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 = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +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/r/R/R-3.1.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb new file mode 100644 index 0000000000..bf05d8f5a0 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb @@ -0,0 +1,392 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', 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('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.9', ext_options), + ('statmod', '1.4.20', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.34.0', bioconductor_options), + ('BiocInstaller', '1.16.2', bioconductor_options), + ('preprocessCore', '1.28.0', bioconductor_options), + ('affy', '1.44.0', bioconductor_options), + ('GO.db', '3.0.0', bioconductor_options), + ('limma', '3.22.7', bioconductor_options), + ('RBGL', '1.42.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.14', ext_options), + ('kohonen', '2.0.15', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.6', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), +] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb new file mode 100644 index 0000000000..9c7b469262 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From 5053bdf739278a69e72aaf37ef1b4aae6713143d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 11:33:17 +0200 Subject: [PATCH 0571/1172] {lang}[foss/2015a] Perl 5.20.2-bare + 5.22.0-bare --- .../p/Perl/Perl-5.20.2-foss-2015b-bare.eb | 17 +++++++++++++++++ .../p/Perl/Perl-5.22.0-foss-2015b-bare.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb new file mode 100644 index 0000000000..429d35babf --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb new file mode 100644 index 0000000000..57a07e49a5 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From 4c881638bb006180987d88ea212e2594cb39dc62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 11:33:36 +0200 Subject: [PATCH 0572/1172] {lang}[intel/2015a] Perl 5.20.2-bare + 5.22.0-bare --- .../p/Perl/Perl-5.20.2-intel-2015b-bare.eb | 17 +++++++++++++++++ .../p/Perl/Perl-5.22.0-intel-2015b-bare.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb new file mode 100644 index 0000000000..82afea03f3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb new file mode 100644 index 0000000000..fb80329ad2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +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] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From d4de047f78ce48453ffb69f7c1368409f5a337a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 14:32:07 +0200 Subject: [PATCH 0573/1172] fix toolchain version --- easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb index fb80329ad2..4eeb6cf7a0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb @@ -5,7 +5,7 @@ versionsuffix = '-bare' homepage = 'http://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.cpan.org/src/5.0'] -- GitLab From 08f63b5b332ad1025372a1ceb9b55b39bd5c7e79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 14:52:02 +0200 Subject: [PATCH 0574/1172] fix bioconductor extension versions --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb index bf05d8f5a0..a3bd99b60e 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From 5e9221c8f7abf3ee210aa51a57950ad2607df0b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 14:52:30 +0200 Subject: [PATCH 0575/1172] fix bioconductor extension versions --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb index d4fb7b27b9..a502672f4e 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From 3e51f5f2725cff3862c1ba285f7f3a1ac14d4a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 15:17:48 +0200 Subject: [PATCH 0576/1172] fix bioconductor extension versions in R 3.1.3 easyconfigs --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index dee61f1e01..b43dc45c25 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 56604be04c..2863ba62ad 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From c76815515fe01591e6d4e2da417e6f39ec2b806c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 15:59:48 +0200 Subject: [PATCH 0577/1172] {bio}[intel/2015a] BLAST+ 2.2.31 --- ...BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..e09b9fd298 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# 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 = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f3470631eee344a40a8b0269574075d4755e585e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 18:57:14 +0200 Subject: [PATCH 0578/1172] bump BiocInstaller version to 1.16.5 (yes, again) --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index b43dc45c25..9a8b027e4b 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 2863ba62ad..8a552002a6 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From 4ae1975f91d64de53400bb6b70d8cc0314cb3857 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 18:57:36 +0200 Subject: [PATCH 0579/1172] bump BiocInstaller version to 1.16.5 (yes, again) --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb index a502672f4e..e1e96bff04 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From f28768d1334fb978af4e92bb1e9471061873a8ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 18:58:06 +0200 Subject: [PATCH 0580/1172] bump BiocInstaller version to 1.16.5 (yes, again) --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb index a3bd99b60e..70a801b84e 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From 12b514b123a5edd98c3e22ef2e63c6483331453b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 10:10:01 +0200 Subject: [PATCH 0581/1172] Update CMake-3.2.3-intel-2015a.eb Add support for https --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index f4cde92c3c..749f4c4ebf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} 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')] sanity_check_paths = { -- GitLab From 0d9dd8cfab56eb2eedb6766bfdb1419a3485c434 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 10:10:49 +0200 Subject: [PATCH 0582/1172] Update CMake-3.2.3-foss-2015a.eb Add support for https --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index c7935c7c64..7129af9cae 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} 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')] sanity_check_paths = { -- GitLab From 186574276214d35a7b25c59c22e2690f0d31f1a9 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:27:05 +0200 Subject: [PATCH 0583/1172] Update CMake-3.2.3-intel-2015a.eb Include deps --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 749f4c4ebf..58afb7efd9 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -14,7 +14,12 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '5.9'), +# ('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')]] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From b7fdd6b7e840e1356693d990577140de2fb0d2cb Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:28:52 +0200 Subject: [PATCH 0584/1172] Update CMake-3.2.3-foss-2015a.eb Added necessary deps --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index 7129af9cae..5a9f80d2eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -14,7 +14,12 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '5.9'), +# ('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')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From c48b197c3c3c17bd41d7be421c08e01ec18712e0 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:29:22 +0200 Subject: [PATCH 0585/1172] Update CMake-3.2.3-intel-2015a.eb typo --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 58afb7efd9..4a3f0c85e2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [('ncurses', '5.9'), # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From 78f2b94ee1c94937ba8fa5a9c2054b475a13d3a5 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 26 Jun 2015 22:33:46 +0200 Subject: [PATCH 0586/1172] samtools 1.7.20, zlib 1.27 --- .../s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb | 33 +++++++++++++++++++ .../z/zlib/zlib-1.2.7-goolf-1.7.20.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..3b814ac535 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.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:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..3ae9b5cf4b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, '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 509116d4d2c064b9406771f2fb3487ff25d86a99 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:15:27 +0200 Subject: [PATCH 0587/1172] new gcc versions --- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 35 +++++++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 40 ++++++++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb new file mode 100644 index 0000000000..750c48766b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.8.5' + +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': 'dummy'} + +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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', +] + +checksums = [ + '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# 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/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb new file mode 100644 index 0000000000..17d5d36aba --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -0,0 +1,40 @@ +name = "GCC" +version = '4.9.3' + +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': 'dummy'} + +mpfr_version = '3.1.2' + +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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +patches = [('mpfr-%s-allpatches-20140630.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 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.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 6628d36b6c33edb7401ba29a0d906238d92eada5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:21:01 +0200 Subject: [PATCH 0588/1172] fix checksum GCC-4.8.5 --- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 750c48766b..8618661532 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -21,7 +21,7 @@ sources = [ ] checksums = [ - '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'bfe56e74d31d25009c8fb55fd3ca7e01', # gcc-4.8.5.tar.gz 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz -- GitLab From a0d9b67b4bc1468d2b41e6a9e980aa100e6c89f2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:22:12 +0200 Subject: [PATCH 0589/1172] checksum update for GCC-4.9.3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index 17d5d36aba..e9b0c252f8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -22,14 +22,14 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ - '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz - '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20140630.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From 7346061a978c8ed33505f60e2764ea0b85738b17 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 15:43:19 +0200 Subject: [PATCH 0590/1172] Fix comment in GCC-4.9.3.eb --- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index e9b0c252f8..759f134bcc 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -29,7 +29,7 @@ checksums = [ '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-20140630.patch + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From 7fc3c1381e9f7021fa9b7243f58360b848f675e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 13:13:25 +0200 Subject: [PATCH 0591/1172] {tools}[dummy] GC3Pie 2.3 --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 109 +++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb new file mode 100644 index 0000000000..796b3ed6d7 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -0,0 +1,109 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# 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/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyver}], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 5186f8794404ad07f22fe97799db922c09b13227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 15:09:02 +0200 Subject: [PATCH 0592/1172] enhance sanity check to also consider lib64 --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 796b3ed6d7..6fee6c35e8 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -99,8 +99,10 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyver}], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } -- GitLab From 26bb656fd47cbd8572b1c796ea92e2d83927f82b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 16:09:59 +0200 Subject: [PATCH 0593/1172] fix remarks --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 3 +-- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 9a8b027e4b..d82c3b8db2 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -389,4 +389,3 @@ exts_list = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 8a552002a6..53bd4b0751 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 68f5cd3c5c07cfe148b3818a02801c6941d3d7b4 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 29 Jun 2015 16:27:02 +0200 Subject: [PATCH 0594/1172] Add snappy support and refer Hadoop to the snappy library. This depends on a forthcoming easyblock update to support 'extra_native_libs' configuration setting in the Hadoop EasyBlock. --- .../h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 3 +++ .../s/snappy/snappy-1.1.2-intel-2015a.eb | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index fea9291ff7..3fee82734e 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,12 +19,15 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), + ('snappy', '1.1.2'), ] dependencies = [(java, javaver)] build_native_libs = True +extra_native_libs = [(snappy, 'lib/libsnappy.so')] + parallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000..a37dfd402f --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.2' + +homepage = 'http://code.google.com/p/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': 'intel', 'version': '2015a'} + +source_urls = ['http://code.google.com/p/snappy/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'lib' + -- GitLab From 8b01fad03cb4feb97a2d4c7a0a5ea87ce53a9872 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 29 Jun 2015 16:50:21 +0200 Subject: [PATCH 0595/1172] Add comments based on @boegel's comments. --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index a37dfd402f..e0cf7edd4c 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -15,8 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['lib/libsnappy.so'], - 'dirs': ['include', 'lib', 'share'] + 'dirs': ['include', 'share'] } moduleclass = 'lib' - -- GitLab From 868c8dedcac263c28882505ea38ead6551b854f6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 29 Jun 2015 17:18:30 +0200 Subject: [PATCH 0596/1172] zlib 1.2.8 --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb index 3b814ac535..695f8c6b45 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb @@ -25,7 +25,7 @@ patches = ['SAMtools-1.1_Makefile.patch'] dependencies = [ ('ncurses', '5.9'), - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] parallel = 1 -- GitLab From a414a99b1855a0fbf55a7f7b91cd144f35602253 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 10:35:36 +0200 Subject: [PATCH 0597/1172] Snappy in quotes. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 3fee82734e..596ca9c73c 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -26,7 +26,7 @@ dependencies = [(java, javaver)] build_native_libs = True -extra_native_libs = [(snappy, 'lib/libsnappy.so')] +extra_native_libs = [('snappy', 'lib/libsnappy.so')] parallel = 1 -- GitLab From e456ff1e2440887f6b45f5d7d350b575e115d4c6 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 11:55:17 +0200 Subject: [PATCH 0598/1172] Point eb at github for snappy (w/ the appropriate commit id for the 1.1.2 release) --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index e0cf7edd4c..2a1ececd20 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.2' +commit = '1ff9be9' homepage = 'http://code.google.com/p/snappy/' description = """Snappy is a compression/decompression library. It does not aim @@ -10,8 +11,8 @@ instead, it aims for very high speeds and reasonable compression.""" toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://code.google.com/p/snappy/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/google/snappy/archive'] +sources = ['%s.tar.gz' % commit] sanity_check_paths = { 'files': ['lib/libsnappy.so'], -- GitLab From 7b476311f62b3081ffddc85c9d1d295ae5a364a5 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 12:13:51 +0200 Subject: [PATCH 0599/1172] Add the snappy toolchain for the Hadoop build dep. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 596ca9c73c..f3a7586e47 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,7 +19,7 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), - ('snappy', '1.1.2'), + ('snappy', '1.1.2', '-intel-2015a'), ] dependencies = [(java, javaver)] -- GitLab From e42a6186b47053238cd92af80fc93a6a502eb8be Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 1 Jul 2015 14:24:06 +0200 Subject: [PATCH 0600/1172] Update cramtools-2.0-Java-1.7.0_80.eb - replaced tabs - removed hard coding in 'modloadmsg' - 'modloadmsg' now declared with single qoutes --- .../easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index 19162420ed..928b078aac 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -19,11 +19,11 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/cramtools-2.0.jar""" +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" sanity_check_paths = { - 'files': ["%(name)s-%(version)s.jar"], - 'dirs': ["lib"] + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] } moduleclass = 'bio' -- GitLab From 6e0f7259e7cce774de924cfc823d795ea26dbe9b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 1 Jul 2015 14:04:39 +0200 Subject: [PATCH 0601/1172] Add preconfigopts to run autogen.sh. Add comment explaining commit id. --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index 2a1ececd20..8e40df0537 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -2,6 +2,10 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.2' + +# 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/' @@ -14,6 +18,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://github.com/google/snappy/archive'] sources = ['%s.tar.gz' % commit] +preconfigopts = "./autogen.sh && " + sanity_check_paths = { 'files': ['lib/libsnappy.so'], 'dirs': ['include', 'share'] -- GitLab From 512a73efaa6900a8beeee17612f223a4e87edc0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jul 2015 17:47:18 +0200 Subject: [PATCH 0602/1172] rename R bundles so they don't conflict on each other --- .../R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb} | 6 +++--- .../R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb} | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/r/{R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb => R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb} (91%) rename easybuild/easyconfigs/r/{R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb => R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb} (98%) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb similarity index 91% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb rename to easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb index 5a2b464944..c20e9fab18 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-devtools' version = '20150520' rver = '3.1.3' -versionsuffix = '-R-%s-devtools' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -16,7 +16,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('R-bundle', '20150323', '-R-%s-extra' % rver), + ('R-bundle-extra', '20150323', '-R-%s' % rver), ] ext_options = { diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb similarity index 98% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb rename to easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb index a6d53af385..96c79b8200 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-extra' version = '20150323' rver = '3.1.3' -versionsuffix = '-R-%s-extra' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -- GitLab From ebebd211cf5b2506febd6bbfb7ad2cc9499ab818 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 13:52:37 +0200 Subject: [PATCH 0603/1172] {chem}[intel/2015a] CP2K 20130228 --- .../b/Bison/Bison-2.7-intel-2015a.eb | 22 ++++++++++++ .../c/CP2K/CP2K-20130228-intel-2015a.eb | 36 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.3-intel-2015a.eb | 34 ++++++++++++++++++ .../f/flex/flex-2.5.37-intel-2015a.eb | 14 ++++++++ 4 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb new file mode 100644 index 0000000000..48aa608e0d --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': '2015a'} + +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/CP2K/CP2K-20130228-intel-2015a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb new file mode 100644 index 0000000000..fd8d96a13d --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb @@ -0,0 +1,36 @@ +name = 'CP2K' +version = '20130228' + +homepage = 'http://cp2k.berlios.de/index.html' +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': '2015a'} +toolchainopts = {'pic': True} + +sources = ['CP2K-%(version)s.tar.gz'] + +patches = [ + 'CP2K-2013_fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +dependencies = [ + ('FFTW', '3.3.3'), + ('Libint', '1.1.4'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb new file mode 100644 index 0000000000..10fd990805 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.3' + +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': '2015a'} +toolchainopts = {'optarch': True, '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' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb new file mode 100644 index 0000000000..086db50be8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From a831b17749160a27620eaa69ffdd267e0ec65d58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 14:21:35 +0200 Subject: [PATCH 0604/1172] add missing patch file --- .../c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..7533a55308 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- cp2k/makefiles/Makefile.orig 2013-02-04 17:55:57.000000000 +0100 ++++ cp2k/makefiles/Makefile 2013-02-05 17:55:06.811020304 +0100 +@@ -200,7 +200,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g'))\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif -- GitLab From 4e756528393d07d55a277f94e495eb10d6849fbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 16:34:01 +0200 Subject: [PATCH 0605/1172] include custom sanity_check_paths for R bundles --- .../R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb | 6 +++++- .../R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb | 5 +++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb index c20e9fab18..aa48ed3b81 100644 --- a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -41,5 +41,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -moduleclass = 'lang' +sanity_check_paths = { + 'files': [], + 'dirs': ['devtools'], +} +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb index 96c79b8200..1bde4e9f5d 100644 --- a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -92,4 +92,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + moduleclass = 'lang' -- GitLab From b0b333fee30fc82e8260523f70695450acc57b42 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Thu, 2 Jul 2015 16:38:32 +0200 Subject: [PATCH 0606/1172] Test dump method on every easyconfig file --- test/easyconfigs/easyconfigs.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 838f4a2957..c9c6efcdfe 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -52,6 +52,7 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS 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.filetools import read_file, write_file # indicates whether all the single tests are OK, @@ -235,7 +236,9 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - # parse easyconfig + ec_orig = read_file(spec) + + # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: ec = ecs[0]['ec'] @@ -250,7 +253,7 @@ def template_easyconfig_test(self, spec): name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # sanity check for software name - self.assertTrue(ec['name'], name) + self.assertTrue(ec['name'], name) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) @@ -297,6 +300,14 @@ def template_easyconfig_test(self, spec): app.close_log() os.remove(app.logfile) + # dump the easyconfig file + ec.dump('test.eb') + dumped_ec = EasyConfig('test.eb') + + self.assertEqual(ec['name'], dumped_ec['name']) + self.assertEqual(ec['version'], dumped_ec['version']) + self.assertEqual(ec['sanity_check_paths'], dumped_ec['sanity_check_paths']) + # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) -- GitLab From adb1f38506c7af0ca7c38c06654c05e0d3afd09a Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Thu, 2 Jul 2015 16:51:12 +0200 Subject: [PATCH 0607/1172] remove unnecessary lines --- test/easyconfigs/easyconfigs.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c9c6efcdfe..744dbffc53 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -52,8 +52,6 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS 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.filetools import read_file, write_file - # indicates whether all the single tests are OK, # and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well @@ -236,8 +234,6 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - ec_orig = read_file(spec) - # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: -- GitLab From 8d5e1eeaf6c0bf445ee150d4cf0dda78bba47c82 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Jul 2015 17:04:47 +0200 Subject: [PATCH 0608/1172] Use only GCC (no toolchain) and use 4th arg for build dep. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- .../{snappy-1.1.2-intel-2015a.eb => snappy-1.1.2-GCC-4.9.2.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/snappy/{snappy-1.1.2-intel-2015a.eb => snappy-1.1.2-GCC-4.9.2.eb} (94%) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index f3a7586e47..e94d4f7d23 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,7 +19,7 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), - ('snappy', '1.1.2', '-intel-2015a'), + ('snappy', '1.1.2', '', ('GCC', '4.9.2')), ] dependencies = [(java, javaver)] diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb similarity index 94% rename from easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb rename to easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb index 8e40df0537..551924427d 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb @@ -13,7 +13,7 @@ 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': 'intel', 'version': '2015a'} +toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['https://github.com/google/snappy/archive'] sources = ['%s.tar.gz' % commit] -- GitLab From c5f9c342a1b75d17942001c136d66b1a04215385 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 09:59:10 +0200 Subject: [PATCH 0609/1172] {lib}[intel/2015a] gensim 0.11.1-1 --- ...nsim-0.11.1-1-intel-2015a-Python-2.7.10.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f497f88541 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.11.1-1' + +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': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'lib' -- GitLab From 5f1cc312d0ce41468705551027478b840742f757 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Fri, 3 Jul 2015 10:18:46 +0200 Subject: [PATCH 0610/1172] dump test full config --- test.eb | 19 +++++++++++++++++++ test/easyconfigs/easyconfigs.py | 14 +++++++++----- 2 files changed, 28 insertions(+), 5 deletions(-) create mode 100644 test.eb diff --git a/test.eb b/test.eb new file mode 100644 index 0000000000..0e62d9dea1 --- /dev/null +++ b/test.eb @@ -0,0 +1,19 @@ +easyblock = "Tarball" + +name = "ABINIT" +version = "7.0.3" +versionsuffix = "-x86_64_linux_gnu4.5" + +homepage = "http://www.abinit.org/" +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = [('abinit-7.0.3_x86_64_linux_gnu4.5.bz2', 'tar xfj %s')] +source_urls = ['http://ftp.abinit.org/'] + + +sanity_check_paths = {'files': ['bin/abinit'], 'dirs': []} + +moduleclass = "chem" \ No newline at end of file diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 744dbffc53..bba0b94318 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -53,6 +53,7 @@ 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 + # indicates whether all the single tests are OK, # and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well # other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 @@ -297,12 +298,15 @@ def template_easyconfig_test(self, spec): os.remove(app.logfile) # dump the easyconfig file - ec.dump('test.eb') - dumped_ec = EasyConfig('test.eb') + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfig(test_ecfile) + os.remove(test_ecfile) - self.assertEqual(ec['name'], dumped_ec['name']) - self.assertEqual(ec['version'], dumped_ec['version']) - self.assertEqual(ec['sanity_check_paths'], dumped_ec['sanity_check_paths']) + for key in sorted(ec._config): + self.assertEqual(ec[key], dumped_ec[key]) # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) -- GitLab From 656407932c9d4c7cd4439366a95c35e45a9a75c1 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Fri, 3 Jul 2015 10:19:31 +0200 Subject: [PATCH 0611/1172] Delete test.eb --- test.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 test.eb diff --git a/test.eb b/test.eb deleted file mode 100644 index 0e62d9dea1..0000000000 --- a/test.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Tarball" - -name = "ABINIT" -version = "7.0.3" -versionsuffix = "-x86_64_linux_gnu4.5" - -homepage = "http://www.abinit.org/" -description = """Abinit is a plane wave pseudopotential code for doing - condensed phase electronic structure calculations using DFT.""" - -toolchain = {'version': 'dummy', 'name': 'dummy'} - -sources = [('abinit-7.0.3_x86_64_linux_gnu4.5.bz2', 'tar xfj %s')] -source_urls = ['http://ftp.abinit.org/'] - - -sanity_check_paths = {'files': ['bin/abinit'], 'dirs': []} - -moduleclass = "chem" \ No newline at end of file -- GitLab From a331bbc485af537c090dab17f425bb59bb5a7ef3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 3 Jul 2015 10:51:32 +0200 Subject: [PATCH 0612/1172] seaborn easyconfig --- ...Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..63cb8346de --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.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 (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'Seaborn' +version = '0.6.0' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/mwaskom/seaborn/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), +] + +moduleclass = 'bio' -- GitLab From 7cfbf96ed8bb6afc4b64c6ad1d4379a4cdba62e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 14:45:25 +0200 Subject: [PATCH 0613/1172] remove exts_filter definition from Python 3.4.3 easyconfig, as it can cause problems --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a71f6ecf62..1aa8ae3172 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -27,7 +27,6 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! # package versions updated Jan 19th 2015 -exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ ('setuptools', '15.2', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], -- GitLab From cfbc6e966d0e64f230d17267a2d2acf8a55a7554 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:18:14 +0200 Subject: [PATCH 0614/1172] style fixes in NEMO easyconfig --- easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb index cc73946e3e..a4b50a7074 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb @@ -2,14 +2,18 @@ name = 'NEMO' version = '3.4' homepage = 'http://www.nemo-ocean.eu/' -description = 'NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies.' +description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for + oceanographic research, operational oceanography seasonal forecast and climate studies.""" toolchain = {'name': 'ictce','version': '6.1.5'} toolchainopts = {'opt': False, 'optarch': False} +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] + with_components = ['OPA_SRC', 'LIM_SRC_3'] add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] -sources = [SOURCELOWER_TAR_GZ] -dependencies = [('netCDF-Fortran', '4.2')] +moduleclass = 'geo' -- GitLab From 2bfb7fd19de8a7fe899f27325032b04071c637bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:22:50 +0200 Subject: [PATCH 0615/1172] include SVN revision in version, add instructions on obtaining sources --- ...MO-3.4-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NEMO/{NEMO-3.4-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5.eb} (72%) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb similarity index 72% rename from easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb rename to easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb index a4b50a7074..27572d3f2a 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb @@ -1,5 +1,5 @@ name = 'NEMO' -version = '3.4' +version = '3.4-r5541' homepage = 'http://www.nemo-ocean.eu/' description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for @@ -8,7 +8,10 @@ description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-o toolchain = {'name': 'ictce','version': '6.1.5'} toolchainopts = {'opt': False, 'optarch': False} -sources = [SOURCELOWER_TAR_GZ] +# authenticated SVN access required +# svn --username 'login' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2012/dev_v3_4_STABLE_2012 +# tar cfvz NEMO-3.4-r.tar.gz dev_v3_4_STABLE_2012 +sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] -- GitLab From 0b52721d54adb12815e6e436ec83bd25fc2f9194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:28:24 +0200 Subject: [PATCH 0616/1172] add missing easyconfigs for (indirect) NEMO dependencies --- .../b/Bison/Bison-2.7-ictce-6.1.5.eb | 22 +++++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb | 18 +++++++++++++ .../f/flex/flex-2.5.37-ictce-6.1.5.eb | 14 ++++++++++ .../h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb | 27 +++++++++++++++++++ .../easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb | 26 ++++++++++++++++++ .../netCDF-Fortran-4.2-ictce-6.1.5.eb | 18 +++++++++++++ .../n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb | 19 +++++++++++++ .../s/Szip/Szip-2.1-ictce-6.1.5.eb | 23 ++++++++++++++++ .../z/zlib/zlib-1.2.7-ictce-6.1.5.eb | 22 +++++++++++++++ 9 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000..deba4d2a79 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..2f5d07d58f --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': '6.1.5'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb new file mode 100644 index 0000000000..15e30d50fb --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb new file mode 100644 index 0000000000..caf75ce765 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '6.1.5'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb new file mode 100644 index 0000000000..062e490de1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.16' + +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': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb new file mode 100644 index 0000000000..87478cf832 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..262ebc70b9 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..d90d48702e --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.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': 'ictce', 'version': '6.1.5'} +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.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000..62b9777b1c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From cf1d950b8751b5ad91981c1a8c87c6cc70ba5884 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 20:31:54 +0200 Subject: [PATCH 0617/1172] fix source_urls in netCDF easyconfigs --- .../n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb | 12 +++++++----- .../n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb | 12 +++++++----- .../n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb | 5 ++++- .../netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-intel-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb | 5 ++++- 23 files changed, 98 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb index e83acc3cca..aaee694b4f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 8bf5c28625..6aa937d650 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb index c00c295552..3d4e4b8034 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb index 4a0335f764..1cf87a93d6 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index eef9aa4fe1..2e121dba81 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb index 827d6154da..8a0164a41a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb index 3f8634ce66..9278dcabb7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb index 738b574b64..70579f3686 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb index b51011ebf8..bf3bcad88f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb index 4f975041bc..8ae8d0db4f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb index a8fa0bc40a..4527973704 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb index 1d208f1301..a518b2a451 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs-mt')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index a43794119f..9caf198302 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb index 5c53c8bf57..081ab64f4b 100755 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb index b2e2392049..59a30799c7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb index 5e5d78307e..a238c0cf33 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb index fa034d1498..69ddb9f9ca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb index dd168910be..741f74cd63 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb index 78d6d431c3..a3bce6fa83 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [('netCDF-4.3.0_nc-config.in.cmake', 'netcdf-4.3.0')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index ffb64828a3..f0b637b12c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb index e42de69332..d7b013c418 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 172783a9aa..e848a71eec 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index 0456d513c3..623ceccdb3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', -- GitLab From 2699d9477fa0ccaacc963980f33a7f9bbcb7403d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 20:41:48 +0200 Subject: [PATCH 0618/1172] fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs --- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb | 5 ++++- .../n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb | 5 ++++- .../netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb | 6 +++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb | 5 ++++- 17 files changed, 69 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb index b46d95de45..e0cfb1558e 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb index 57f1d3e4bb..d47cb17c75 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('netCDF', '4.2.1.1', versionsuffix), diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb index 7a7c4b81bc..400224b911 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb index 3b4f3e5332..16ea5317c4 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb index de008bf235..d8cdaf41c4 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb index 091c9e9f89..adc9cf91dc 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb index f4a44d81d3..2caeeaf083 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb @@ -5,11 +5,15 @@ 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': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb index a8cbfe5ddb..bd158f66c5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb index fac88a30ba..d4ddc1b2b5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb index 6b36f2c00b..b50fb138ef 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1', versionsuffix)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb index ef015a9175..40fd553f1f 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb index 4686402139..09084630c1 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb index b0bef7e67a..f7f72fcd32 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb index 4d00f104ad..c51e1a7941 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb index d623122642..9b2aa29afe 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb index 59ed0da09a..7823a5fa7d 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb index ed31b043f1..39adb73d6e 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] -- GitLab From dc66e3f090c96e10fbdcd51f477c5afa1fc8cf7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jul 2015 11:01:49 +0200 Subject: [PATCH 0619/1172] {tools}[dummy] GC3Pie 2.4.0 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb new file mode 100644 index 0000000000..8a1d9386f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.0' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From affa6314feea3d9c3c71163a58f072edb5d1c282 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 11:09:34 +0300 Subject: [PATCH 0620/1172] Contributing Biggus Python Package --- ...Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 22 +++++++++++++++++++ .../Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..46e8bcb1a8 --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.11.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..4374be186c --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.5.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' -- GitLab From f8984993b96be359549b82b1029abc6363621590 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 12:42:09 +0300 Subject: [PATCH 0621/1172] Contributing BSMAP --- .../b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 35 +++++++++ easybuild/easyconfigs/b/BSMAP/makefile.patch | 19 +++++ easybuild/easyconfigs/b/BSMAP/param.patch | 7 ++ easybuild/easyconfigs/b/BSMAP/samtools.patch | 76 +++++++++++++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/BSMAP/makefile.patch create mode 100644 easybuild/easyconfigs/b/BSMAP/param.patch create mode 100644 easybuild/easyconfigs/b/BSMAP/samtools.patch diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb new file mode 100644 index 0000000000..51f6971d10 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'BSMAP' +version = '2.74' + +homepage = 'https://code.google.com/p/bsmap/' +description = """BSMAP is a short reads mapping software for bisulfite sequencing reads.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bsmap.googlecode.com/files/'] +sources = [SOURCELOWER_TGZ] + +skipsteps = ['configure'] + +installopts = "INSTALL_DIR=%(installdir)s" + +patches = [ + 'makefile.patch', + 'param.patch', + 'samtools.patch', +] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), + ('SAMtools', '0.1.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BSMAP/makefile.patch b/easybuild/easyconfigs/b/BSMAP/makefile.patch new file mode 100644 index 0000000000..f015ee9ecd --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/makefile.patch @@ -0,0 +1,19 @@ +--- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 ++++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 +@@ -1,6 +1,6 @@ + CC= g++ + +-BIN = $(DESTDIR)/usr/bin ++BIN=$(INSTALL_DIR)/bin + FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 + #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 + +@@ -16,7 +16,7 @@ + bsmap: $(OBJS1) + (cd samtools; make) + (cd gzstream; make) +- $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream ++ $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -L$(EBROOTZLIB)/lib -lz -lgzstream + rm -f *.o + + clean: diff --git a/easybuild/easyconfigs/b/BSMAP/param.patch b/easybuild/easyconfigs/b/BSMAP/param.patch new file mode 100644 index 0000000000..8c645688c9 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/param.patch @@ -0,0 +1,7 @@ +--- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 ++++ param.cpp 2014-12-08 22:14:20.305028000 +0200 +@@ -1,3 +1,4 @@ ++#include + #include "param.h" + #include + diff --git a/easybuild/easyconfigs/b/BSMAP/samtools.patch b/easybuild/easyconfigs/b/BSMAP/samtools.patch new file mode 100644 index 0000000000..714b79ef91 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/samtools.patch @@ -0,0 +1,76 @@ +--- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 ++++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 +@@ -10,10 +10,11 @@ + bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ + cut_target.o phase.o bam2depth.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-#LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses ++ + + .SUFFIXES:.c .o + +@@ -44,10 +45,10 @@ + $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -73,10 +74,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ +--- bsmap-2.74/samtools/misc/Makefile.orig 2012-09-20 23:01:58.000000000 +0300 ++++ bsmap-2.74/samtools/misc/Makefile 2014-12-15 14:40:50.817493925 +0200 +@@ -28,13 +28,13 @@ + lib: + + seqtk:seqtk.o +- $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ seqtk.o -lm -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -43,10 +43,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz +- ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz ++ + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c -- GitLab From fe4db4b4391463e47a4ac55d4c89955fc3bec529 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 11:47:52 +0200 Subject: [PATCH 0622/1172] include URL with info on supported keys, sort alphabetically --- easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb index 27572d3f2a..fd8734e64f 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb @@ -15,8 +15,9 @@ sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] +# see http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 with_components = ['OPA_SRC', 'LIM_SRC_3'] -add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] -del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] +add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] +del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] moduleclass = 'geo' -- GitLab From bb9e83280daf1aa47ddf729ee80530b420693e60 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 12:53:42 +0300 Subject: [PATCH 0623/1172] Contributing mpi4py python package built with Python 3.2.3 --- .../mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000..f3694ef966 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3' + +homepage = 'https://code.google.com/p/mpi4py/' +description = """MPI for Python (mpi4py) provides bindings of the +Message Passing Interface (MPI) standard for the Python programming +language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + BITBUCKET_DOWNLOADS, + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'mpi' -- GitLab From b1d8483fd7f29470bfe757f95d467d56a4cb5d1f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 7 Jul 2015 12:22:21 +0200 Subject: [PATCH 0624/1172] Glob the lib so. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index e94d4f7d23..0b189ca56d 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -26,7 +26,7 @@ dependencies = [(java, javaver)] build_native_libs = True -extra_native_libs = [('snappy', 'lib/libsnappy.so')] +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] parallel = 1 -- GitLab From bcf3bf0075d0dd1edab559f4914c5b29e12f138e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 12:23:18 +0200 Subject: [PATCH 0625/1172] add IC3 versionsuffix to NEMO easyconfig, clarify add_keys/del_keys --- ...1-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5-IC3.eb} | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/n/NEMO/{NEMO-3.4-r5541-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5-IC3.eb} (67%) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb similarity index 67% rename from easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb rename to easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb index fd8734e64f..3f22d89443 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb @@ -1,5 +1,6 @@ name = 'NEMO' version = '3.4-r5541' +versionsuffix = '-IC3' homepage = 'http://www.nemo-ocean.eu/' description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for @@ -15,8 +16,13 @@ sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] -# see http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 +# setting specific to IC3 +# enable ocean model and Louvain-la-Neuve sea-ice model +# see http://www.nemo-ocean.eu/About-NEMO with_components = ['OPA_SRC', 'LIM_SRC_3'] +# enable LIM3, MPI, IOM, global ORCA config at 1 degree resolution (& more) +# disable LIM2, global ORCA config at 2 degree resolution, tides induced vertical mixing +# see http://www.nemo-ocean.eu/About-NEMO, http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] -- GitLab From a473b3bc317f55f0bc63566b218cbb8ceee7000f Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 14:38:31 +0300 Subject: [PATCH 0626/1172] Changing patch files names --- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 6 +++--- .../{makefile.patch => BSMAP-2.74_makefile-modif.patch} | 3 +++ .../BSMAP/{param.patch => BSMAP-2.74_parameters-cpp.patch} | 2 ++ .../{samtools.patch => BSMAP-2.74_samtools-deps.patch} | 2 ++ 4 files changed, 10 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/b/BSMAP/{makefile.patch => BSMAP-2.74_makefile-modif.patch} (80%) rename easybuild/easyconfigs/b/BSMAP/{param.patch => BSMAP-2.74_parameters-cpp.patch} (69%) rename easybuild/easyconfigs/b/BSMAP/{samtools.patch => BSMAP-2.74_samtools-deps.patch} (96%) diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index 51f6971d10..e7342e0349 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -16,9 +16,9 @@ skipsteps = ['configure'] installopts = "INSTALL_DIR=%(installdir)s" patches = [ - 'makefile.patch', - 'param.patch', - 'samtools.patch', + 'BSMAP-2.74_makefile-modif.patch', + 'BSMAP-2.74_parameters-cpp.patch', + 'BSMAP-2.74_samtools-deps.patch', ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BSMAP/makefile.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch similarity index 80% rename from easybuild/easyconfigs/b/BSMAP/makefile.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch index f015ee9ecd..7992065109 100644 --- a/easybuild/easyconfigs/b/BSMAP/makefile.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -1,3 +1,6 @@ +Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to +the correct location of the ZLIB libraries +Thekla Loizou July 2015 --- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 +++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 @@ -1,6 +1,6 @@ diff --git a/easybuild/easyconfigs/b/BSMAP/param.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch similarity index 69% rename from easybuild/easyconfigs/b/BSMAP/param.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch index 8c645688c9..21007be7d3 100644 --- a/easybuild/easyconfigs/b/BSMAP/param.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch @@ -1,3 +1,5 @@ +Patch to include unitstd.h in the parameters for cpp +Thekla Loizou July 2015 --- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 +++ param.cpp 2014-12-08 22:14:20.305028000 +0200 @@ -1,3 +1,4 @@ diff --git a/easybuild/easyconfigs/b/BSMAP/samtools.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch similarity index 96% rename from easybuild/easyconfigs/b/BSMAP/samtools.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch index 714b79ef91..7475b92e92 100644 --- a/easybuild/easyconfigs/b/BSMAP/samtools.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch @@ -1,3 +1,5 @@ +Patch to point to the correct locations of SAMTools dependencies +Thekla Loizou July 2015 --- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 +++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 @@ -10,10 +10,11 @@ -- GitLab From e54e5fe645a618e2f859c00abb0f1a34a7acb693 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:13:31 +0300 Subject: [PATCH 0627/1172] Contributing ordereddict Python package --- ...dereddict-1.1-goolf-1.4.10-Python-2.7.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..5fe608081a --- /dev/null +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'ordereddict' +version = '1.1' + +homepage = 'https://pypi.python.org/pypi/ordereddict' +description = """Drop-in substitute for Py2.7's new collections.OrderedDict. +The recipe has big-oh performance that matches regular dictionaries (amortized +O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/o/%s/' % name.lower()] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': [], + 'dirs': ['.'], +} + +moduleclass = 'data' -- GitLab From 98ef6b15062ccb5baf74000731b4769b0146b5c7 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:28:30 +0300 Subject: [PATCH 0628/1172] Contriburing rpy2 Python Package --- .../rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb | 25 +++++++++++++++++++ .../rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..aeaed8d595 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000..6d5edb8ec2 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' -- GitLab From b609405807703f4192290fc9a85a0cb2e67edfac Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:39:29 +0300 Subject: [PATCH 0629/1172] Contributing Pyke Python Package --- .../Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..2453963f18 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Pyke' +version = '1.1.1' + +homepage = 'http://sourceforge.net/projects/pyke/' +description = """Pyke introduces a form of Logic Programming (inspired by Prolog) +to the Python community by providing a knowledge-based inference engine +(expert system) written in 100% Python.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +moduleclass = 'data' -- GitLab From 6a574354c714fe1dcb9534050b737f94a882bb07 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 16:06:25 +0300 Subject: [PATCH 0630/1172] Changes in easyconfig file --- .../ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb index 5fe608081a..a404ae249a 100644 --- a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing)."" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/o/%s/' % name.lower()] +source_urls = ['http://pypi.python.org/packages/source/o/%(namelower)s'] sources = [SOURCELOWER_TAR_GZ] python = "Python" @@ -21,9 +21,4 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} - moduleclass = 'data' -- GitLab From e53a62536f35adaf79819b1aabe1a4cafc7bfddf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 19:09:00 +0200 Subject: [PATCH 0631/1172] {perf}[intel/2015a] OSU Micro-Benchmarks v4.4.1 --- .../OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb new file mode 100644 index 0000000000..43857d07e3 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '4.4.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +configopts = 'CC="$MPICC"' + +modextrapaths = {'PATH': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']]} + +sanity_check_paths = { + 'files': [], + 'dirs': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']], +} + +moduleclass = 'perf' -- GitLab From afa53f5a6e78c96dc445141db44f006a28c54cce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 21:23:19 +0200 Subject: [PATCH 0632/1172] fix remarks --- .../OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb index 43857d07e3..d96cc487d5 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -9,15 +9,16 @@ description = """OSU Micro-Benchmarks""" toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$MPICC"' -modextrapaths = {'PATH': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']]} +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': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']], + 'dirs': benchmark_dirs, } moduleclass = 'perf' -- GitLab From 933b3512596586cc396eda8173c4dd00a48ec830 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 8 Jul 2015 09:44:29 +0300 Subject: [PATCH 0633/1172] Changes to config file and makefile patch --- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index e7342e0349..1318374418 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] skipsteps = ['configure'] -installopts = "INSTALL_DIR=%(installdir)s" +installopts = "DESTDIR=%(installdir)s" patches = [ 'BSMAP-2.74_makefile-modif.patch', diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch index 7992065109..daf84a74d5 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -1,5 +1,5 @@ Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to -the correct location of the ZLIB libraries +to the correct location of the ZLIB libraries Thekla Loizou July 2015 --- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 +++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 @@ -7,7 +7,7 @@ Thekla Loizou July 2015 CC= g++ -BIN = $(DESTDIR)/usr/bin -+BIN=$(INSTALL_DIR)/bin ++BIN = $(DESTDIR)/bin FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 -- GitLab From ecd27c7f809de416f719c86e86a9e13cfc4483e6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Jul 2015 11:09:47 +0200 Subject: [PATCH 0634/1172] Add minimal example easyconfig for SystemCompiler easyblock --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-system.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb new file mode 100644 index 0000000000..c90402823f --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -0,0 +1,19 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +## + +easyblock = 'SystemCompiler' + +name = "GCC" +version = "system" + +homepage = "" +description = "" # will be defined by the SystemCompiler easyblock when left empty or provide a custom description + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +moduleclass = 'compiler' -- GitLab From d2b7c9d32b3abff832ecd422f67352139ebec88a Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Jul 2015 17:18:32 +0200 Subject: [PATCH 0635/1172] Provide homepage/description info in easyconfig file as requested --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index c90402823f..dcad754e21 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -11,8 +11,9 @@ easyblock = 'SystemCompiler' name = "GCC" version = "system" -homepage = "" -description = "" # will be defined by the SystemCompiler easyblock when left empty or provide a custom description +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': 'dummy'} -- GitLab From 1620ca0634c3d85fb783b99d8272484e3f2ccb0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 17:39:28 +0200 Subject: [PATCH 0636/1172] disable FTGL support, since it requires Mesa... --- .../easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb index f239ad58fc..e763143dc4 100644 --- a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.2.3')] start_dir = 'eman2' separate_build_dir = True -configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" sanity_check_paths = { 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', -- GitLab From af12ebae5b8619a6346f2c199fd972028c97c99c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 19:14:08 +0200 Subject: [PATCH 0637/1172] disable FTGL support in all EMAN2 easyconfigs, since it requires Mesa... --- .../easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb index b7a9c16a5a..82523c603b 100644 --- a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.2.3')] start_dir = 'eman2' separate_build_dir = True -configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" sanity_check_paths = { 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', -- GitLab From 603e52db023817ae3dbc772d90f3a85677ff1009 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 20:14:48 +0200 Subject: [PATCH 0638/1172] include comment w.r.t. 'system' version --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index dcad754e21..2d2a4ac6aa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -8,10 +8,13 @@ easyblock = 'SystemCompiler' -name = "GCC" -version = "system" +name = 'GCC' +# using 'system' as a version instructs the SystemCompiler easyblock to derive the actual compiler version, +# and define $EBVERSION* accordingly (yet generate a module named GCC/system); +# if an actual version is specified here, it will be checked against the version of the system compiler that was found +version = 'system' -homepage = "http://gcc.gnu.org/" +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,...).""" -- GitLab From 363dfde20b1a4031792a0c6b6f3c5138f8233a37 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 9 Jul 2015 08:57:49 +0200 Subject: [PATCH 0639/1172] added Gtkmm and dependencies --- .../a/ATK/ATK-2.16.0-intel-2015a.eb | 27 +++++++++++++++++++ .../a/Atkmm/Atkmm-2.22.7-intel2015a.eb | 26 ++++++++++++++++++ .../c/cairo/cairo-1.14.2-intel-2015a.eb | 27 +++++++++++++++++++ .../c/cairomm/cairomm-1.10.0-intel-2015a.eb | 26 ++++++++++++++++++ .../g/GLibmm/GLibmm-2.41.2-intel-2015a.eb | 24 +++++++++++++++++ .../g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb | 27 +++++++++++++++++++ .../gdk-pixbuf-2.31.4-intel-2015a.eb | 26 ++++++++++++++++++ .../g/gtk+/gtk+-2.24.28-intel-2015a.eb | 22 +++++++++++++++ .../h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb | 26 ++++++++++++++++++ .../libsigc++/libsigc++-2.4.1-intel-2015a.eb | 21 +++++++++++++++ .../p/Pango/Pango-1.37.1-intel-2015a.eb | 21 +++++++++++++++ .../p/Pangomm/Pangomm-2.36.0-intel-2015a.eb | 26 ++++++++++++++++++ 12 files changed, 299 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb new file mode 100644 index 0000000000..6fc5e6597f --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.16.0' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), +] + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb b/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb new file mode 100644 index 0000000000..946d69a7a2 --- /dev/null +++ b/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Atkmm' +version = '2.22.7' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + Atkmm is the official C++ interface for the ATK accessibility toolkit library. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLibmm', '2.41.2'), + ('ATK', '2.16.0'), +] + +sanity_check_paths = { + 'files': ['lib/libatkmm-1.6.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb new file mode 100644 index 0000000000..86f4a27b8e --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.2' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('bzip2', '1.0.6'), +] + +# 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/c/cairomm/cairomm-1.10.0-intel-2015a.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb new file mode 100644 index 0000000000..5aa8ded5d6 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "cairomm" +version = '1.10.0' + +homepage = 'http://cairographics.org' +description = """ + The Cairomm package provides a C++ interface to Cairo. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('cairo', '1.14.2'), + ('libsigc++', '2.4.1'), +] + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.0.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb new file mode 100644 index 0000000000..9102a3d424 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GLibmm' +version = '2.41.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '%(version)s'), + ('libsigc++', '2.4.1'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.4.so'], + 'dirs': [], +} +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb new file mode 100644 index 0000000000..8e1cb764c0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Gtkmm' +version = '2.24.4' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The Gtkmm package provides a C++ interface to GTK+ 2. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Atkmm', '2.22.7'), + ('gtk+', '2.24.28'), + ('Pangomm', '2.36.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgtkmm-2.4.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb new file mode 100644 index 0000000000..3d4350cb57 --- /dev/null +++ b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' +name = 'gdk-pixbuf' +version = '2.31.4' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), + ('libjpeg-turbo', '1.4.0'), + ('libpng', '1.6.16'), + ('LibTIFF', '4.0.3'), + +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb new file mode 100644 index 0000000000..289385029d --- /dev/null +++ b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gtk+' +version = '2.24.28' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.16.0'), + ('gdk-pixbuf', '2.31.4'), + ('Pango', '1.37.1'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb new file mode 100644 index 0000000000..407a30edff --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '0.9.41' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['HarfBuzz_no_symbolic.patch'] + +dependencies = [ + ('cairo', '1.14.2'), + ('GLib', '2.41.2'), +] + +sanity_check_paths = { + 'files': ["lib/libharfbuzz.so"], + 'dirs': [""], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb new file mode 100644 index 0000000000..966ef00954 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.4.1' + +homepage = 'http://www.gtk.org/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(name)s/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +sanity_check_paths = { + 'files': ['lib/libsigc-2.0.so'], + 'dirs': [], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb new file mode 100644 index 0000000000..78e015464a --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' +name = 'Pango' +version = '1.37.1' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), + ('cairo', '1.14.2'), + ('HarfBuzz', '0.9.41'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb new file mode 100644 index 0000000000..044fc1c671 --- /dev/null +++ b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Pangomm' +version = '2.36.0' + +homepage = 'http://www.pango.org/' +description = """ The Pangomm package provides a C++ interface to Pango. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLibmm', '2.41.2'), + ('cairomm', '1.10.0'), + ('Pango', '1.37.1'), +] + + +sanity_check_paths = { + 'files': ['lib/libpangomm-1.4.so'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 086adc2bb1f51059273334bcc2fcba73066f98c9 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 9 Jul 2015 10:06:01 +0300 Subject: [PATCH 0640/1172] Contrib Trim Galore --- .../t/Trim_Galore/Trim_Galore-0.3.7.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb new file mode 100644 index 0000000000..594ab520d4 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb @@ -0,0 +1,28 @@ +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.3.7' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply +quality and adapter trimming to FastQ files, with some extra functionality for +MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.10.1', '-Java-1.7.0_21'), + ('cutadapt', '1.5', '-goolf-1.4.10-Python-2.7.3'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f1e45bb7484fec30c6f3469fa71a128d6382ba40 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 9 Jul 2015 11:10:33 +0200 Subject: [PATCH 0641/1172] added HarfBuzz_no_symbolic.patch --- .../easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch new file mode 100644 index 0000000000..95722f9e5e --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch @@ -0,0 +1,11 @@ +--- configure.orig 2013-07-02 16:46:02.548302080 +0200 ++++ configure 2013-07-02 16:47:50.428410650 +0200 +@@ -16342,7 +16342,7 @@ + if test "x$GCC" = "xyes"; then + + # Make symbols link locally +- LDFLAGS="$LDFLAGS -Bsymbolic-functions" ++ LDFLAGS="$LDFLAGS" # -Bsymbolic-functions" + + # Make sure we don't link to libstdc++ + CXXFLAGS="$CXXFLAGS -fno-rtti -fno-exceptions" -- GitLab From 2719283b4e177ceb77c35e07d8310795bd9417aa Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 9 Jul 2015 11:15:26 +0200 Subject: [PATCH 0642/1172] Added missing dependencies --- ...el2015a.eb => Atkmm-2.22.7-intel-2015a.eb} | 0 .../g/GLib/GLib-2.41.2-intel-2015a.eb | 19 ++++++++++++ .../l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb | 30 +++++++++++++++++++ 3 files changed, 49 insertions(+) rename easybuild/easyconfigs/a/Atkmm/{Atkmm-2.22.7-intel2015a.eb => Atkmm-2.22.7-intel-2015a.eb} (100%) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb b/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel2015a.eb rename to easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb new file mode 100644 index 0000000000..f484250400 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb @@ -0,0 +1,19 @@ +name = 'GLib' +version = '2.41.2' +easyblock = 'ConfigureMake' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" +toolchain = {'name': 'intel', 'version': '2015a'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.8')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb new file mode 100644 index 0000000000..5b2c252b76 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -0,0 +1,30 @@ +## +# 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 = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 2a1ed4a93d9ba0752c396db910673fe1cc2d7198 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jul 2015 21:37:24 +0200 Subject: [PATCH 0643/1172] fix typo --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index 2d2a4ac6aa..b24177d713 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -14,7 +14,7 @@ name = 'GCC' # if an actual version is specified here, it will be checked against the version of the system compiler that was found version = 'system' -homepage = 'http://gcc.gnu.org/" +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,...).""" -- GitLab From f0b8df35e7cb76b9be3667a3c24d93ec15bcd160 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Fri, 10 Jul 2015 10:27:37 +0300 Subject: [PATCH 0644/1172] Adding dependencies for Trim Galore --- .../cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb | 33 ++++++++++++++++ .../f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb | 39 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..76d2e9cb85 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://cutadapt.googlecode.com/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb new file mode 100644 index 0000000000..2a3c309f90 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb @@ -0,0 +1,39 @@ +## +# 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 +# License:: MIT/GPL +# +## +easyblock = "PackedBinary" + +name = 'FastQC' +version = '0.10.1' + +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': 'dummy'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +java = 'Java' +javaver = '1.7.0_21' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" + +sanity_check_paths = { + 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", + "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], + 'dirs': ["Contaminants", "Help", "Templates", "uk"], +} + +moduleclass = 'bio' -- GitLab From a9cf7a544cb111145bffc25c3da39623d6378fc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 10:26:31 +0200 Subject: [PATCH 0645/1172] rename to R-bundle-pbd --- .../R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 5 ++--- .../pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 0 2 files changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/{R-bundle => R-bundle-pbd}/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb (93%) rename easybuild/easyconfigs/r/{R-bundle => R-bundle-pbd}/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch (100%) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb similarity index 93% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb rename to easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb index 05e79faaa5..347e7c8f1e 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -1,10 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-pbd' version = '20150605' -bundlename = 'pbd' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) +versionsuffix = '-R-%s-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch similarity index 100% rename from easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch rename to easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch -- GitLab From 9fd3633bc392130237f3b8c67fdc943c9d3e5ffc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 11:25:21 +0200 Subject: [PATCH 0646/1172] fix typo --- .../r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb index 347e7c8f1e..002b4a69ed 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -3,7 +3,7 @@ easyblock = 'Bundle' name = 'R-bundle-pbd' version = '20150605' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -- GitLab From a4ef0fa2041d1624f9c5932f87fdd443f73804a3 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 10 Jul 2015 12:59:00 +0200 Subject: [PATCH 0647/1172] Delete zlib-1.2.7-goolf-1.7.20.eb --- .../z/zlib/zlib-1.2.7-goolf-1.7.20.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb deleted file mode 100644 index 3ae9b5cf4b..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -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': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, '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 8c2daaba9f64292d87f2addc7c30961628485101 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 13:00:10 +0200 Subject: [PATCH 0648/1172] {system}[*/2015a] OpenSSL 1.0.1p --- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 24 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb 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 new file mode 100644 index 0000000000..ca15409515 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': '2015a'} +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-%(version)s_fix-parallel.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' 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 new file mode 100644 index 0000000000..8317b28f02 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': 'intel', 'version': '2015a'} +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-%(version)s_fix-parallel.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 7108f2596f827aee80af6fbf9e140c9c44edb975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 13:02:48 +0200 Subject: [PATCH 0649/1172] fix patch specs in OpenSSL 1.0.1p easyconfigs --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 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 ca15409515..7f6643b5da 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 @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.1m_icc-fixes.patch', + 'OpenSSL-1.0.1m_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] 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 8317b28f02..99325fdaf7 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 @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.1m_icc-fixes.patch', + 'OpenSSL-1.0.1m_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From c2a0de6109218b7c7c77afcaf6866907b3e50371 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Fri, 10 Jul 2015 16:30:58 +0300 Subject: [PATCH 0650/1172] Applying toolchain changes --- ....10.1-Java-1.7.0_21.eb => FastQC-0.10.1-goolf-1.4.10.eb} | 5 ++--- ...im_Galore-0.3.7.eb => Trim_Galore-0.3.7-goolf-1.4.10.eb} | 6 +++--- 2 files changed, 5 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/FastQC/{FastQC-0.10.1-Java-1.7.0_21.eb => FastQC-0.10.1-goolf-1.4.10.eb} (90%) rename easybuild/easyconfigs/t/Trim_Galore/{Trim_Galore-0.3.7.eb => Trim_Galore-0.3.7-goolf-1.4.10.eb} (82%) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb similarity index 90% rename from easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb rename to easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb index 2a3c309f90..bd99041b10 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb @@ -17,16 +17,15 @@ It reads in sequence data in a variety of formats and can either provide an inte 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': 'dummy'} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] java = 'Java' javaver = '1.7.0_21' -versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_21', '', True)] install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb similarity index 82% rename from easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb rename to easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 594ab520d4..425d2e339b 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -8,7 +8,7 @@ description = """A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] @@ -16,8 +16,8 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '-Java-1.7.0_21'), - ('cutadapt', '1.5', '-goolf-1.4.10-Python-2.7.3'), + ('FastQC', '0.10.1'), + ('cutadapt', '1.5', '-Python-2.7.3'), ] sanity_check_paths = { -- GitLab From bc738e41f70dc3c772033ac47fc9b9129b75d582 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Jul 2015 10:39:21 +0200 Subject: [PATCH 0651/1172] style fixes in CMake easyconfigs --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 8 +++++--- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index 5a9f80d2eb..e6f905f409 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -14,9 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9'), -# ('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 +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')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 4a3f0c85e2..5e1447f0f0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -14,9 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9'), -# ('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 +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')] -- GitLab From 9135c9396f881a39102710e627dcedfb91e61bf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Jul 2015 14:07:47 +0200 Subject: [PATCH 0652/1172] fix patches for OpenSSL 1.0.1p --- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch | 100 ++++++++++++++++++ 3 files changed, 102 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch 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 7f6643b5da..6800732437 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-1.0.1m_icc-fixes.patch', - 'OpenSSL-1.0.1m_fix-parallel.patch', -] +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] dependencies = [('zlib', '1.2.8')] 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 99325fdaf7..9e06d07cee 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 @@ -12,10 +12,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = [ - 'OpenSSL-1.0.1m_icc-fixes.patch', - 'OpenSSL-1.0.1m_fix-parallel.patch', -] +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch new file mode 100644 index 0000000000..4609252d6d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch @@ -0,0 +1,100 @@ +diff -ru openssl-1.0.1p.orig/Configure openssl-1.0.1p/Configure +--- openssl-1.0.1p.orig/Configure 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/Configure 2015-07-11 14:02:52.000000000 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1p.orig/crypto/aes/aes_x86core.c openssl-1.0.1p/crypto/aes/aes_x86core.c +--- openssl-1.0.1p.orig/crypto/aes/aes_x86core.c 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/aes/aes_x86core.c 2015-07-11 14:02:52.000000000 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/des/des_locl.h openssl-1.0.1p/crypto/des/des_locl.h +--- openssl-1.0.1p.orig/crypto/des/des_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/des/des_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h openssl-1.0.1p/crypto/rc5/rc5_locl.h +--- openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/rc5/rc5_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From 3ead61ff878dde0a4fb678d7a2f9f78bbe92ea00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Jul 2015 00:07:18 +0200 Subject: [PATCH 0653/1172] style fixes in eudev easyconfigs --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 4 ++-- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index 3efae98cdb..a1c5928f0b 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -20,10 +20,10 @@ builddependencies = [ ('gperf', '3.0.4'), ] -osdependencies = [('kernel-headers','linux-libc-dev')] +osdependencies = [('kernel-headers', 'linux-libc-dev')] configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' -preinstallopts = "make check && " +runtest = 'check' sanity_check_paths = { 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb index 9ada9135c9..5108981bdd 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -20,10 +20,10 @@ builddependencies = [ ('gperf', '3.0.4'), ] -osdependencies = [('kernel-headers','linux-libc-dev')] +osdependencies = [('kernel-headers', 'linux-libc-dev')] configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' -preinstallopts = "make check && " +runtest = 'check' sanity_check_paths = { 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], -- GitLab From 7df1044fa78375edf24fcade7b335439bb3ace0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:16:45 +0200 Subject: [PATCH 0654/1172] rename BuildEnv-defaults to buildenv-default --- .../b/BuildEnv/BuildEnv-defaults-intel-2015a.eb | 13 ------------- .../b/buildenv/buildenv-default-intel-2015a.eb | 13 +++++++++++++ 2 files changed, 13 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb deleted file mode 100644 index 7e91b365f2..0000000000 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = "BuildEnv" - -name = 'BuildEnv' -version = 'defaults' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you - can use to easily transition between toolchains when building your software. To query the variables being set please use: - module show """ - -toolchain = {'name': 'intel', 'version': '2015a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb new file mode 100644 index 0000000000..0321acfcc5 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' -- GitLab From d23a37d802a66b777295ea800ab349c1077efaa7 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Jul 2015 12:34:55 +0200 Subject: [PATCH 0655/1172] Reintroduce tabs into patch file. --- ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch index ae54615b78..34eaf4da13 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch +++ b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -1,45 +1,45 @@ # Add support for intel mpi by removing references to BI_COMM_WORLD # BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. ---- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 -+++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 @@ -25,7 +25,9 @@ - BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; - BLACS_APTS.BI_MyContxts = BI_MyContxts; - BLACS_APTS.BI_SysContxts = BI_SysContxts; + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; +#ifndef __INTEL_COMPILER - BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; +#endif - BLACS_APTS.BI_Stats = BI_Stats; + BLACS_APTS.BI_Stats = BI_Stats; - #if (BLACS_APTS_DEBUG & 1) == 1 + #if (BLACS_APTS_DEBUG & 1) == 1 @@ -44,7 +46,9 @@ - BI_AuxBuff.nAops, BI_AuxBuff.N); - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); +#ifndef __INTEL_COMPILER - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, +#endif - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); @@ -89,7 +93,9 @@ - BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; - BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; +#ifndef __INTEL_COMPILER - BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; +#endif - BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; - #if (BLACS_APTS_DEBUG & 1) == 1 + #if (BLACS_APTS_DEBUG & 1) == 1 @@ -109,7 +115,9 @@ - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, +#ifndef __INTEL_COMPILER - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); +#endif - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); - } + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } -- GitLab From b6efe47eda0ac187c3b843fb2d47080ec4eb67dd Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Jul 2015 12:45:40 +0200 Subject: [PATCH 0656/1172] Remove old file path. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 ------------------- ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 ------------------- 2 files changed, 90 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb delete mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb deleted file mode 100644 index 05e79faaa5..0000000000 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle' -version = '20150605' -bundlename = 'pbd' -rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [ - ('R', rver), -] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -exts_list = [ - ('pbdMPI', '0.2-5', ext_options), - ('pbdSLAP', '0.2-0', ext_options), - ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), - ('pbdDMAT', '0.2-3', ext_options), - ('pbdDEMO', '0.2-0', ext_options), - ('pmclust', '0.1-6', ext_options), - ('EMCluster', '0.2-4', ext_options), -] - -modextrapaths = {'R_LIBS': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch deleted file mode 100644 index ae54615b78..0000000000 --- a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch +++ /dev/null @@ -1,45 +0,0 @@ -# Add support for intel mpi by removing references to BI_COMM_WORLD -# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. ---- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 -+++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 -@@ -25,7 +25,9 @@ - BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; - BLACS_APTS.BI_MyContxts = BI_MyContxts; - BLACS_APTS.BI_SysContxts = BI_SysContxts; -+#ifndef __INTEL_COMPILER - BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; -+#endif - BLACS_APTS.BI_Stats = BI_Stats; - - #if (BLACS_APTS_DEBUG & 1) == 1 -@@ -44,7 +46,9 @@ - BI_AuxBuff.nAops, BI_AuxBuff.N); - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); -+#ifndef __INTEL_COMPILER - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, -+#endif - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); -@@ -89,7 +93,9 @@ - - BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; - BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; -+#ifndef __INTEL_COMPILER - BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; -+#endif - BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; - - #if (BLACS_APTS_DEBUG & 1) == 1 -@@ -109,7 +115,9 @@ - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, -+#ifndef __INTEL_COMPILER - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); -+#endif - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); - } - -- GitLab From 642bfe59dfeade76094a635195dbf906d704d6e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:51:14 +0200 Subject: [PATCH 0657/1172] include Tcl/Tk dependencies in R 3.2.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb index cf66631597..fb02153585 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] exts_list = [] -- GitLab From 030501ad94e6cb0e4ba7f90aae463c4e8852cb1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:59:53 +0200 Subject: [PATCH 0658/1172] add Tcl/Tk as dependencies in R 3.2.0 easyconfig --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 ++ .../t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 93ecdc515d..69f979e2b7 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..e2124cc24d --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +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-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000..5d72cc8d79 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From e220e175644efd2cb8194a7498a195808f11e7fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 13:15:55 +0200 Subject: [PATCH 0659/1172] bump versions of Bioconductor pkgs --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 53 +++++++++---------- 1 file changed, 25 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 69f979e2b7..7c7cafbc81 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -219,16 +219,16 @@ exts_list = [ ('R.matlab', '3.2.0', ext_options), ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.0', bioconductor_options), - ('IRanges', '2.2.1', bioconductor_options), - ('GenomeInfoDb', '1.4.0', bioconductor_options), - ('AnnotationDbi', '1.30.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.0', bioconductor_options), - ('GenomicRanges', '1.20.3', bioconductor_options), - ('Rsamtools', '1.20.1', bioconductor_options), - ('BiocParallel', '1.2.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), @@ -310,19 +310,19 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.1', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), - ('affy', '1.46.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.1', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.0', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), ('KEGG.db', '3.1.2', bioconductor_options), ('annaffy', '1.40.0', bioconductor_options), ('gcrma', '2.40.0', bioconductor_options), ('oligoClasses', '1.30.0', bioconductor_options), - ('edgeR', '3.10.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), @@ -365,7 +365,7 @@ exts_list = [ ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.10.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), @@ -376,25 +376,22 @@ exts_list = [ ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), ('biomaRt', '2.24.0', bioconductor_options), - ('annotate', '1.46.0', bioconductor_options), - ('GSEABase', '1.30.1', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), - ('Category', '2.34.0', bioconductor_options), - ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.2', bioconductor_options), - ('GenomicFeatures', '1.20.0', bioconductor_options), - ('BSgenome', '1.36.0', bioconductor_options), - ('VariantAnnotation', '1.14.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.0', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), - ('DESeq2', '1.8.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), - ('genefilter', '1.50.0', bioconductor_options), - ('affycoretools', '1.40.1', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), ('Homo.sapiens', '1.1.2', bioconductor_options), ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), @@ -408,13 +405,13 @@ exts_list = [ ('KEGGprofile', '1.10.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), - ('lumi', '2.20.1', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), ('tkWidgets', '1.46.0', bioconductor_options), ('Mfuzz', '2.28.0', bioconductor_options), ('maSigPro', '1.40.0', bioconductor_options), ('SPIA', '2.20.0', bioconductor_options), - ('Gviz', '1.12.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), -- GitLab From d7e28ea23262a7532e44dde55a0035e59890567a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:27:22 +0200 Subject: [PATCH 0660/1172] bump version of hgu133plus2.db --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 7c7cafbc81..28b28e0dba 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -347,7 +347,7 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.1.2', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), -- GitLab From 38d5bbb0bef54572add45272316cf5dc36fdf076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:48:17 +0200 Subject: [PATCH 0661/1172] split off Bioconductor packages into a separate easyconfig --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 93 ------------------- 1 file changed, 93 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 28b28e0dba..4395bd8986 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -33,18 +33,6 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} # !! order of packages is important !! @@ -217,21 +205,6 @@ exts_list = [ ('cgdsr', '1.1.33', ext_options), ('R.utils', '2.0.1', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.14.0', bioconductor_options), - ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), - ('IRanges', '2.2.5', bioconductor_options), - ('GenomeInfoDb', '1.4.1', bioconductor_options), - ('AnnotationDbi', '1.30.1', bioconductor_options), - ('XVector', '0.8.0', bioconductor_options), - ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), - ('GenomicRanges', '1.20.5', bioconductor_options), - ('Rsamtools', '1.20.4', bioconductor_options), - ('BiocParallel', '1.2.9', bioconductor_options), - ('GenomicAlignments', '1.4.1', bioconductor_options), - ('ShortRead', '1.26.0', bioconductor_options), - ('graph', '1.46.0', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), ('Formula', '1.2-1', ext_options), @@ -309,32 +282,13 @@ exts_list = [ ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), - ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), - ('preprocessCore', '1.30.0', bioconductor_options), - ('affy', '1.46.1', bioconductor_options), - ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), - ('RBGL', '1.44.0', bioconductor_options), - ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.1', bioconductor_options), - ('KEGG.db', '3.1.2', bioconductor_options), - ('annaffy', '1.40.0', bioconductor_options), - ('gcrma', '2.40.0', bioconductor_options), - ('oligoClasses', '1.30.0', bioconductor_options), - ('edgeR', '3.10.2', bioconductor_options), - ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), - ('baySeq', '2.2.0', bioconductor_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), - ('qvalue', '2.0.0', bioconductor_options), - ('impute', '1.42.0', bioconductor_options), ('matrixStats', '0.14.0', ext_options), ('samr', '2.0', ext_options), - ('DEGseq', '1.22.0', bioconductor_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), @@ -347,72 +301,25 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.1.3', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('illuminaio', '0.10.0', bioconductor_options), ('registry', '0.2', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), - ('bumphunter', '1.8.0', bioconductor_options), - ('multtest', '2.24.0', bioconductor_options), - ('siggenes', '1.42.0', bioconductor_options), ('nleqslv', '2.7', ext_options), - ('DynDoc', '1.46.0', bioconductor_options), - ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.12.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), - ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), - ('RNASeqPower', '1.8.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), - ('biomaRt', '2.24.0', bioconductor_options), - ('annotate', '1.46.1', bioconductor_options), - ('GSEABase', '1.30.2', bioconductor_options), - ('genefilter', '1.50.0', bioconductor_options), - ('Category', '2.34.2', bioconductor_options), - ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), - ('VariantAnnotation', '1.14.6', bioconductor_options), - ('biovizBase', '1.16.0', bioconductor_options), - ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), - ('geneplotter', '1.46.0', bioconductor_options), - ('DESeq2', '1.8.1', bioconductor_options), - ('ReportingTools', '2.8.0', bioconductor_options), - ('affycoretools', '1.40.5', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), - ('Homo.sapiens', '1.1.2', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.18.0', bioconductor_options), - ('GenomeGraphs', '1.28.0', bioconductor_options), - ('geneLenDataBase', '1.4.0', bioconductor_options), - ('goseq', '1.20.0', bioconductor_options), ('httr', '0.6.1', ext_options), - ('KEGGREST', '1.8.0', bioconductor_options), - ('KEGGgraph', '1.26.0', bioconductor_options), - ('KEGGprofile', '1.10.0', bioconductor_options), - ('minfi', '1.14.0', bioconductor_options), - ('methylumi', '2.14.0', bioconductor_options), - ('lumi', '2.20.2', bioconductor_options), - ('widgetTools', '1.46.0', bioconductor_options), - ('tkWidgets', '1.46.0', bioconductor_options), - ('Mfuzz', '2.28.0', bioconductor_options), - ('maSigPro', '1.40.0', bioconductor_options), - ('SPIA', '2.20.0', bioconductor_options), - ('Gviz', '1.12.1', bioconductor_options), - ('cummeRbund', '2.10.0', bioconductor_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), ('tensor', '1.5', ext_options), -- GitLab From acdd5f8ffc2be122a82d57e81f307d25da1ef9cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:49:51 +0200 Subject: [PATCH 0662/1172] actually add R-bundle-Bioconductor easyconfig --- ...e-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 124 ++++++++++++++++++ 1 file changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb new file mode 100644 index 0000000000..88053df714 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -0,0 +1,124 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.0' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + +moduleclass = 'lang' -- GitLab From 374ade892abc2308b2275c28f24f31e06e406ce8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:58:14 +0200 Subject: [PATCH 0663/1172] fix sanity check --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 88053df714..2e05c29673 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -118,7 +118,7 @@ modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': ['RCurl', 'XML', 'spliceR'], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], } moduleclass = 'lang' -- GitLab From 7d4512368e615e99bd4e4205a62a576ed8628421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:02:31 +0200 Subject: [PATCH 0664/1172] downgrade Java to 1.7.0_80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 4395bd8986..0b3a34bd3f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] -- GitLab From e8a33bbd0b50c0b42eec0ed235c4135cf7126001 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:08:36 +0200 Subject: [PATCH 0665/1172] {lang}[dummy] Java 1.8.0_45 --- easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb new file mode 100644 index 0000000000..50a687a050 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_45' + +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 726b83763fcf15e22faa18698cf3847ce89dbc3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:10:28 +0200 Subject: [PATCH 0666/1172] {lib}[intel/2015a] libjpeg-turbo 1.4.1 --- .../libjpeg-turbo-1.4.1-intel-2015a.eb | 24 ++++++++++++++ .../n/NASM/NASM-2.11.08-intel-2015a.eb | 31 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb new file mode 100644 index 0000000000..3f922516d9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +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': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb new file mode 100644 index 0000000000..77ceaa2d9a --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.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 = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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 6d9d4dc75af37146c1c9658db60af889c5b7270b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:36:56 +0200 Subject: [PATCH 0667/1172] add cURL/libxml2 deps + RCurl lib --- .../c/cURL/cURL-7.43.0-goolf-1.7.20.eb | 29 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 4 ++- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8a52b67eb0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': 'goolf', 'version': '1.7.20'} + +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" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 0b3a34bd3f..c303899088 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -22,6 +22,8 @@ dependencies = [ ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -329,8 +331,8 @@ exts_list = [ ('rgeos', '0.3-8', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), - ] moduleclass = 'lang' -- GitLab From 40fbd81ee8900e43f38100d1b7723ee78655e065 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:41:30 +0200 Subject: [PATCH 0668/1172] add missing deps --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb | 28 ++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000..e4763fc7a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': '2015a'} + +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" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..906e3a297c --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +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': '1.7.20'} + +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')] + +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 722898b7de41ab85e827519c6713a8403a439e9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:44:50 +0200 Subject: [PATCH 0669/1172] kick out cURL intel/2015a easyconfig --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb deleted file mode 100644 index e4763fc7a1..0000000000 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cURL' -version = '7.43.0' - -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': '2015a'} - -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" - -sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'tools' -- GitLab From 02b044da3f765afa44b268f0cbcea3afd05c0182 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:45:57 +0200 Subject: [PATCH 0670/1172] add OpenSSL easyconfig --- .../o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb 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 new file mode 100644 index 0000000000..2e714a6aff --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': '1.7.20'} +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'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 0cc773f51fc1999c9e19b57e8fb3a42bb94adbba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:46:49 +0200 Subject: [PATCH 0671/1172] {lang}[intel/2015a] R v3.2.1 --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 ++ .../easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 340 ++++++++++++++++++ 2 files changed, 369 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000..e4763fc7a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': '2015a'} + +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" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000..cd0b403c28 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -0,0 +1,340 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-10', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-34', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.1.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('scales', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.16-0', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.3', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('shiny', '0.12.1', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.7-0', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', ext_options), + ('samr', '2.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('FactoMineR', '1.31.3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', 'Finite', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('XML', '3.98-1.3', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('rgeos', '0.3-11', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('doParallel', '1.0.8', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' -- GitLab From 4ff33aeeb65ac1304c47a5205defa099ec495690 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 21:45:27 +0200 Subject: [PATCH 0672/1172] fix flexmix version in R 3.2.1 easyconfig --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index cd0b403c28..4600a51eeb 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -297,7 +297,7 @@ exts_list = [ ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), - ('flexmix', 'Finite', ext_options), + ('flexmix', '2.3-13', ext_options), ('prabclus', '2.2-6', ext_options), ('diptest', '0.75-7', ext_options), ('trimcluster', '0.1-2', ext_options), -- GitLab From ad0f2adaaf4baab4a102e1060f25e5fedce7d11a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:21:37 +0200 Subject: [PATCH 0673/1172] add patch for geometry R extension + add missing extensions (fpp & co) --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 4600a51eeb..33b6f91f96 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -56,7 +56,7 @@ exts_list = [ ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), @@ -335,6 +335,10 @@ exts_list = [ ('bio3d', '2.2-2', ext_options), ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From 5233500a63dc309fd18132cfa53ad185b69b67e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:34:30 +0200 Subject: [PATCH 0674/1172] fix templating issues --- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb | 2 +- easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 5cdf92f035..fa154ada7f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index 49d7098c87..558ae70b7f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 6de0d3d8d3..0464a3968b 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 46c998562c..c9298da39e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index b955c4abf7..8d4de54b7a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index c9f730872f..fa2a08d015 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 6866cddf63..fa449b6641 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 1ed83c4526..7dc3787320 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 3f65089c09..436dd9a680 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index d22d8136b3..9346ee7b4c 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['SOURCEFORGE_SOURCE'] +source_urls = [SOURCEFORGE_SOURCE] builddependencies = [ ('Bison', '3.0.2'), diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb index 5101540bd3..0ad7f07069 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb @@ -32,7 +32,7 @@ dependencies = [ # RELION expects FLTK to be in external/fltk-1.3.0 configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " sanity_check_paths = { 'files': ['bin/relion'], diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb index 7b003f1cbf..25abcbdcb9 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' # users expect the maingui binary to be called relion -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " moduleclass = 'bio' -- GitLab From bd8efd374826612f5e577a4e176d82c182f67fa0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:43:56 +0200 Subject: [PATCH 0675/1172] add extensions that dropped out --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index c303899088..0b8d49ad4e 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -320,6 +320,11 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ('XML', '3.98-1.1', ext_options), ('httr', '0.6.1', ext_options), ('maptools', '0.8-36', ext_options), -- GitLab From e9890996ac06f8717cfb8d767c3fc63dc126c34f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:44:56 +0200 Subject: [PATCH 0676/1172] add missing vegan extension --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 33b6f91f96..602865ae41 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -320,6 +320,11 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), @@ -335,10 +340,6 @@ exts_list = [ ('bio3d', '2.2-2', ext_options), ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From d10f4cf170b7f8b6af9350c8c1ca42f373863ed1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:50:45 +0200 Subject: [PATCH 0677/1172] drop patch in OpenSSL, not need when icc is not used in toolchain --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 2 -- 1 file changed, 2 deletions(-) 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 2e714a6aff..733ddd9ac4 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 @@ -12,8 +12,6 @@ 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'] - dependencies = [('zlib', '1.2.8')] runtest = 'test' -- GitLab From f16a42c06203e45ec1326184dd2a73a0f4252221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:29:13 +0200 Subject: [PATCH 0678/1172] bump version to 2.2.0 and update release notes --- RELEASE_NOTES | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b593156524..da12db80a1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -4,7 +4,57 @@ 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 3,689 easyconfig files, for 611 different software packages, -33 different (compiler) toolchains and 8 software bundles. +33 different (compiler) toolchains and 12 software bundles. + +v2.2.0 (July 14th 2015) +----------------------- + +feature + bugfix release +- added example easyconfig files for XXX new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), frealign (#1619), FPM (#1440), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), libXScrnSaver (#1653), MATIO (#1004), MuTect *#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) +- added easyconfigs for 4 new software bundles: + R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) +- added easyconfigs for new GNU toolchain (#1346, #1669) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, + Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 +- various other enhancements, including: + - update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337) + - update PDT easyconfigs to use PDT easyblock (#1687) + - add custom sanity_check_paths in libxml2 easyconfigs (#1690) + - enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761) + - include snappy as dependency in Hadoop easyconfigs (#1758, #1773) + - enable SSL support in CMake v3.2.3 easyconfigs (#1784) + - add additional extensions in R easyconfigs (#1637) +- various bug fixes, including: + - add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631) + - fix issue with OpenMPI dependency in ECore easyconfigs (#777) + - don't run the Bloom tests for Jellyfish, they can randomly fail (#1016) + - fix source URLs in BioPerl easyconfigs (#1075) + - patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576) + - consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722) + - include Tcl and Tk as dependencies in R easyconfig (#1623) + - add patch for installing paycheck as Py3 extension (#1629) + - add Perl dependency in git 2.x easyconfigs (#1631) + - fix easycofnig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) + - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) + - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) + - drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657) + - include missing libxml2 dep in GLib easyconfigs (#1666) + - fix source URLs in Qt easyconfigs (#1673) + - fix source URLs for argparse Python extension (#1697) + - fix source URLs for deap Python extension (#1699) + - fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708) + - fix names for Xmipp easyconfigs and patches (#1719) + - add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734) + - add M4 as build dep for GCC 5.1.0 (#1735) + - fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748) + - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) + - fix source_urls in netCDF easyconfigs (#1766) + - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) + - add Infiniband-related patch for OpenMPI versions < 1.8.6 (#1785) v2.1.1 (May 18th 2015) ---------------------- diff --git a/setup.py b/setup.py index 9e5dd5137c..d9262a0b8c 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0dev' +VERSION = '2.2.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 8a6e8a5b0788bd4f277d2ab72540ce96bb161362 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:30:39 +0200 Subject: [PATCH 0679/1172] move up lmtest, as dep for vcd --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 602865ae41..89ab03d55c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -151,6 +151,7 @@ exts_list = [ ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-4', ext_options), ('sp', '1.1-1', ext_options), + ('lmtest', '0.9-34', ext_options), ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), ('rpart', '4.1-10', ext_options), @@ -180,7 +181,6 @@ exts_list = [ ('xts', '0.9-7', ext_options), ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-34', ext_options), ('mnormt', '1.5-3', ext_options), ('mvtnorm', '1.0-2', ext_options), ('pcaPP', '1.9-60', ext_options), -- GitLab From 9b2749fd7256544007f553f30660f52be6785250 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:33:05 +0200 Subject: [PATCH 0680/1172] move up zoo, as dep for lmtest --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 89ab03d55c..f64a491a30 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -151,6 +151,7 @@ exts_list = [ ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-4', ext_options), ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), ('lmtest', '0.9-34', ext_options), ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), @@ -177,7 +178,6 @@ exts_list = [ ('gamlss.dist', '4.3-4', ext_options), ('hwriter', '1.3.2', ext_options), ('KernSmooth', '2.23-15', ext_options), - ('zoo', '1.7-12', ext_options), ('xts', '0.9-7', ext_options), ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), -- GitLab From 4e23b214781e1f190c912e01f53c004ac0f42784 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:52:20 +0200 Subject: [PATCH 0681/1172] move up munsell/labeling --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index f64a491a30..a5380b8605 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -213,12 +213,12 @@ exts_list = [ ('acepack', '1.3-3.3', ext_options), ('reshape2', '1.4.1', ext_options), ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), ('scales', '0.2.5', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), ('Hmisc', '3.16-0', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), -- GitLab From 0dd9bb204b19b0fc0a267d9e8dc7253a05c0f296 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:57:06 +0200 Subject: [PATCH 0682/1172] move up gridExtra --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index a5380b8605..0c80677c6d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -218,6 +218,7 @@ exts_list = [ ('scales', '0.2.5', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), + ('gridExtra', '0.9.1', ext_options), ('Hmisc', '3.16-0', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), @@ -285,7 +286,6 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), -- GitLab From f46c1223efc8c5df3417884adb358a505ecbcfdd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:13:17 +0200 Subject: [PATCH 0683/1172] add missing NMF/irlba deps, move their deps up --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 0c80677c6d..646fb4f5a1 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -223,6 +223,11 @@ exts_list = [ ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), ('igraph', '1.0.1', ext_options), ('GeneNet', '1.2.12', ext_options), ('ape', '3.3', ext_options), @@ -307,9 +312,6 @@ exts_list = [ ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), ('nleqslv', '2.8', ext_options), ('RGCCA', '2.0', ext_options), -- GitLab From bb5969ead81c891446748fc4b0cf38091001e1f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:18:13 +0200 Subject: [PATCH 0684/1172] add gridBase, move up doParallel --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 646fb4f5a1..413d380137 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -226,6 +226,8 @@ exts_list = [ ('registry', '0.3', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), ('NMF', '0.20.6', ext_options), ('irlba', '1.0.3', ext_options), ('igraph', '1.0.1', ext_options), @@ -340,7 +342,6 @@ exts_list = [ ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), - ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), ] -- GitLab From 666cf6905a7dfa95766de03025cf08511f51b92f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:28:32 +0200 Subject: [PATCH 0685/1172] add jsonlite --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 413d380137..2cb1e9b537 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -240,6 +240,7 @@ exts_list = [ ('ROCR', '1.0-7', ext_options), ('httpuv', '1.3.2', ext_options), ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), -- GitLab From aa767358b1103742d8e0ea15f3102c37be96fb5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:46:16 +0200 Subject: [PATCH 0686/1172] add adegenet deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 2cb1e9b537..85720a0c5d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -242,6 +242,11 @@ exts_list = [ ('R6', '2.1.0', ext_options), ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.4.2', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), ('adephylo', '1.1-6', ext_options), -- GitLab From d403b56c642ab75fe52df69101e5e1faf7ff7fd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:48:49 +0200 Subject: [PATCH 0687/1172] fix assertthat version --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 85720a0c5d..f37c4bc47d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -244,7 +244,7 @@ exts_list = [ ('shiny', '0.12.1', ext_options), ('seqinr', '3.1-3', ext_options), ('spdep', '0.5-88', ext_options), - ('assertthat', '0.4.2', ext_options), + ('assertthat', '0.1', ext_options), ('lazyeval', '0.1.10', ext_options), ('dplyr', '0.4.2', ext_options), ('adegenet', '2.0.0', ext_options), -- GitLab From 7649c009f38c35f6d04708575594aa54dd7cf7c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:52:41 +0200 Subject: [PATCH 0688/1172] add spdep deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index f37c4bc47d..51322416bd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -243,6 +243,8 @@ exts_list = [ ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), ('spdep', '0.5-88', ext_options), ('assertthat', '0.1', ext_options), ('lazyeval', '0.1.10', ext_options), -- GitLab From 59bdc78453640062a6f54af024e7e770329cb574 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:23:19 +0200 Subject: [PATCH 0689/1172] add rgl ext --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 51322416bd..1f1123a8c7 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -268,6 +268,7 @@ exts_list = [ ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), ('labdsv', '1.7-0', ext_options), ('MatrixModels', '0.4-0', ext_options), ('stabs', '0.5-1', ext_options), -- GitLab From 21a9f81921a5c0f34790f2f9cdf816c476ffa3ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:31:50 +0200 Subject: [PATCH 0690/1172] add yaml --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 1f1123a8c7..46cbd47517 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -290,6 +290,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), ('knitr', '1.10.5', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), -- GitLab From aaf7ec0d7712fb2cf216366c40d4a35291407b66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:39:25 +0200 Subject: [PATCH 0691/1172] drop samr, since it depens on Bioconductor --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 46cbd47517..492d9b5716 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -307,7 +307,6 @@ exts_list = [ ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), ('matrixStats', '0.14.2', ext_options), - ('samr', '2.0', ext_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), -- GitLab From aa89237a9e040e0e693692e0e504d4ed883eb75e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:19:32 +0200 Subject: [PATCH 0692/1172] add car/flashClust deps for FactoMineR --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 492d9b5716..196ee6a36f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,6 +310,10 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('car', '2.0-25', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), -- GitLab From a48170785308288724b5f686cd8fed1f9e0c96a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:27:47 +0200 Subject: [PATCH 0693/1172] fix order --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 196ee6a36f..7dabbdcc65 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,9 +310,9 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), - ('car', '2.0-25', ext_options), ('lme4', '1.1-8', ext_options), ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), -- GitLab From 6330576b2372a02447342082e8625e096f3b9b08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:39:47 +0200 Subject: [PATCH 0694/1172] add nloptr --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 7dabbdcc65..041f63b861 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,6 +310,7 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), ('lme4', '1.1-8', ext_options), ('pbkrtest', '0.4-2', ext_options), ('car', '2.0-25', ext_options), -- GitLab From 0f9fb3ba09d9586218b5b8e2607e56278ff51b20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 08:39:30 +0200 Subject: [PATCH 0695/1172] fix name for R-bundle-pbd easyconfig --- ...-3.1.3-pbd.eb => R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/R-bundle-pbd/{R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb => R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb} (100%) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb similarity index 100% rename from easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb rename to easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb -- GitLab From edb6061ee8b9b196dc76f1201f9389ac29d9dc26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:27:46 +0200 Subject: [PATCH 0696/1172] add curl + deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 041f63b861..96599e54e5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,6 +344,12 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('testthat', '0.10.0', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('rmarkdown, '0.7', ext_options), + ('magrittr', '1.5', ext_options), + ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), -- GitLab From a83c33dc766682a152ef0155acb2752dda1e3782 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:39:58 +0200 Subject: [PATCH 0697/1172] fix typo --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 96599e54e5..939bd1e78d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -347,7 +347,7 @@ exts_list = [ ('testthat', '0.10.0', ext_options), ('memoise', '0.2.1', ext_options), ('crayon', '1.3.1', ext_options), - ('rmarkdown, '0.7', ext_options), + ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), -- GitLab From c0f2fd75e84a1eb5539fe0e9afcda5c93d4b6212 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:44:08 +0200 Subject: [PATCH 0698/1172] fix order --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 939bd1e78d..67bf63337f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,9 +344,9 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), ('memoise', '0.2.1', ext_options), - ('crayon', '1.3.1', ext_options), ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), -- GitLab From 06470814d4182c197b08e684b02de918d089765a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:48:15 +0200 Subject: [PATCH 0699/1172] fix order, again --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 67bf63337f..3da3b71713 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,9 +344,9 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), - ('memoise', '0.2.1', ext_options), ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), -- GitLab From e8a99a2087c096ed93adc8e2c1c98542756e98b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:13:25 +0200 Subject: [PATCH 0700/1172] add custom sanity check --- .../R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb index 002b4a69ed..dd2dee5fb4 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -41,4 +41,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} +sanity_check_paths = { + 'files': [], + 'dirs': ['EMCluster', 'pbdBASE', 'pbdDEMO', 'pbdDMAT', 'pbdMPI', 'pbdSLAP', 'pmclust'], +} + moduleclass = 'lang' -- GitLab From ccc171bf66166ca4428839498c2e6812bcda86bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:46:23 +0200 Subject: [PATCH 0701/1172] add stringi, move up magrittr --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 3da3b71713..fd8abad242 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -110,6 +110,8 @@ exts_list = [ ('sendmailR', '1.2-1', ext_options), ('spam', '1.0-1', ext_options), ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), ('stringr', '1.0.0', ext_options), ('evaluate', '0.7', ext_options), ('logspline', '2.1.8', ext_options), @@ -348,7 +350,6 @@ exts_list = [ ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), ('rmarkdown', '0.7', ext_options), - ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), -- GitLab From b529a373011f6be328cb1c0b0898b135d39376e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:51:29 +0200 Subject: [PATCH 0702/1172] remove rgeos, has external dep --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index fd8abad242..20d9840616 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -358,7 +358,6 @@ exts_list = [ ('polyclip', '1.3-2', ext_options), ('goftest', '1.0-3', ext_options), ('spatstat', '1.42-2', ext_options), - ('rgeos', '0.3-11', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), -- GitLab From cfed94972dc3b6c8337df17429de3781521bdc7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:56:17 +0200 Subject: [PATCH 0703/1172] define $CURL_INCLUDES in cURL easyconfig --- easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb index e4763fc7a1..2dbc140a53 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -21,6 +21,8 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # dependencies = [('OpenSSL', '1.0.1p')] # configopts = "--with-ssl=$EBROOTOPENSSL" +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], 'dirs': ['lib/pkgconfig'], -- GitLab From 2d9d81315b72ef06676c77a13cfad990a7d10c76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:58:51 +0200 Subject: [PATCH 0704/1172] move R libs up to resolve dep issues --- easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb index 8a52b67eb0..f234e4353b 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -21,6 +21,8 @@ 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.so'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 0b8d49ad4e..abc5b98de0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -213,12 +213,12 @@ exts_list = [ ('acepack', '1.3-3.3', ext_options), ('reshape2', '1.4.1', ext_options), ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), ('scales', '0.2.4', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), ('Hmisc', '3.15-0', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-45', ext_options), ('data.table', '1.9.4', ext_options), @@ -264,6 +264,7 @@ exts_list = [ ('polspline', '1.1.9', ext_options), ('TH.data', '1.0-6', ext_options), ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), ('rms', '4.3-0', ext_options), ('RWekajars', '3.7.12-1', ext_options), ('RWeka', '0.4-24', ext_options), @@ -273,6 +274,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), ('knitr', '1.10', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), @@ -285,7 +287,6 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), @@ -333,7 +334,6 @@ exts_list = [ ('polyclip', '1.3-0', ext_options), ('goftest', '1.0-2', ext_options), ('spatstat', '1.41-1', ext_options), - ('rgeos', '0.3-8', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), -- GitLab From 351750493fd1895a2e4d6725d913d5ce63abf770 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:04:50 +0200 Subject: [PATCH 0705/1172] add missing AUC ext --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 20d9840616..2c0d705058 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -362,6 +362,7 @@ exts_list = [ ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), ('interpretR', '0.2.3', ext_options), ] -- GitLab From d463c0b4200cc0c7571f64a03414d068023f90b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:33:05 +0200 Subject: [PATCH 0706/1172] {mpi}[iccifort/2015.3.187] impi 5.1.0.079 (or .038?) --- .../impi-5.1.0.038-iccifort-2015.3.187.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..fb7853e6f5 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb @@ -0,0 +1,20 @@ +name = 'impi' +version = '5.1.0.079' + +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': '2015.3.187'} + +# source tarball doesn't match actual version?! +sources = ['l_mpi_p_5.1.0.038.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From c3a871a3d72106546b582e802ec0cb5379ef9613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:56:27 +0200 Subject: [PATCH 0707/1172] no mca_common_sm in OpenMPI 1.4.5 w/ ictce/5.5.0 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index c95534677f..70d3c85032 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -26,7 +26,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] 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], -- GitLab From aff33db32783674ae05e280613771d2288eb1647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:03:08 +0200 Subject: [PATCH 0708/1172] fix easyconfig filename --- ...cifort-2015.3.187.eb => impi-5.1.0.079-iccifort-2015.3.187.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/impi/{impi-5.1.0.038-iccifort-2015.3.187.eb => impi-5.1.0.079-iccifort-2015.3.187.eb} (100%) diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb similarity index 100% rename from easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb rename to easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb -- GitLab From 3797f7040c0b36f78a86a1191cfbb0db036fb4aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:33:57 +0200 Subject: [PATCH 0709/1172] move samr to R-bundle-Bioconductor, where it belongs --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 2e05c29673..27d1fa3cbd 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -112,6 +112,7 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), + ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index abc5b98de0..809e9331c0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -291,7 +291,6 @@ exts_list = [ ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), ('matrixStats', '0.14.0', ext_options), - ('samr', '2.0', ext_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), -- GitLab From 618b9e8cba4ad3d4afbef207d804139d1c9b032e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:35:20 +0200 Subject: [PATCH 0710/1172] {bio}[intel/2015a] Bioconductor 3.1 bundle for R 3.2.1 --- ...le-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb new file mode 100644 index 0000000000..f8eef1d152 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -0,0 +1,125 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.1' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('samr', '2.0', ext_options), # requires impute +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 0717fece3bb0ab591bf32096d3499cf92c51425d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:35:51 +0200 Subject: [PATCH 0711/1172] change moduleclass for R-bundle-Bioconductor to 'bio' --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 27d1fa3cbd..76380a1f11 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -122,4 +122,4 @@ sanity_check_paths = { 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], } -moduleclass = 'lang' +moduleclass = 'bio' -- GitLab From e1ddeb8ade75bfda67f6d7b5d3195cc7bca48b1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:46:49 +0200 Subject: [PATCH 0712/1172] comment out Rmpi --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 809e9331c0..e180920b15 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -53,7 +53,8 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + # Rmpi segfaults (on some systems) when built with goolf/1.7.20? + #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-5', ext_options), -- GitLab From 5a6a70f9b4032f7387fe136ca6a6696551dccbcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:43:10 +0200 Subject: [PATCH 0713/1172] include ext_options definition --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index f8eef1d152..c74f4d7cd1 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -16,6 +16,15 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [('R', rver)] +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', @@ -25,7 +34,7 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_tmpl': name_tmpl, } # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -- GitLab From 4fbe0215f69860552f776419d4bea605f0edd595 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:43:50 +0200 Subject: [PATCH 0714/1172] include ext_options definition in Bioconductor easyconfig --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 76380a1f11..4d24094c6b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -16,6 +16,15 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [('R', rver)] +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', @@ -25,7 +34,7 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_tmpl': name_tmpl, } # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -- GitLab From d0fbdbfb1f7864e0738eeede3c967e5173a786c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:52:42 +0200 Subject: [PATCH 0715/1172] add futile.logger dep for BiocParallel --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index c74f4d7cd1..a79c96313b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -51,6 +51,7 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), -- GitLab From 2f05c60d67f6d5468253b0d50ca8c42c4ddc3d28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:00:30 +0200 Subject: [PATCH 0716/1172] add deps for futile.logger --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index a79c96313b..17cc903943 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -51,6 +51,8 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), -- GitLab From 33bca956c364e1e2e7340dd5aa02bc7ac98e53b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:14:40 +0200 Subject: [PATCH 0717/1172] include perm --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 17cc903943..a93886919a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -73,6 +73,7 @@ exts_list = [ ('oligoClasses', '1.30.0', bioconductor_options), ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), -- GitLab From 7cac100e34dd5ae66369ac868fc46662ae3c288a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:29:15 +0200 Subject: [PATCH 0718/1172] move up samr --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index a93886919a..062278968b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -77,6 +77,7 @@ exts_list = [ ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), -- GitLab From f392ebf6ea616c5dba2436d2a7353679e6ccc424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:06:05 +0200 Subject: [PATCH 0719/1172] fix counts + long line --- RELEASE_NOTES | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index da12db80a1..bfb73bccb6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,19 +3,30 @@ 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 3,689 easyconfig files, for 611 different software packages, -33 different (compiler) toolchains and 12 software bundles. +The latest version of easybuild-easyconfig provides 4,053 easyconfig files, for 673 different software packages, +34 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.2.0 (July 14th 2015) ----------------------- feature + bugfix release -- added example easyconfig files for XXX new software packages: - ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), frealign (#1619), FPM (#1440), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), libXScrnSaver (#1653), MATIO (#1004), MuTect *#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) +- added example easyconfig files for 62 new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), + Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), + EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440), + frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), + GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), + libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), + ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), + Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), + rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), + SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), + VampirServer (#512), verifyBamID (#1675) - added easyconfigs for 4 new software bundles: R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) - added easyconfigs for new GNU toolchain (#1346, #1669) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added example easyconfig for generating buildenv module (#1503) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 -- GitLab From 0c163b787dd72de6937da66cd422edbd36b79e54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:08:57 +0200 Subject: [PATCH 0720/1172] move up GenomicFeatures --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 062278968b..4d63b897fb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,6 +81,7 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -96,7 +97,6 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), -- GitLab From c3fd5250e3fac5929e75752a1ddf5778685aaa47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:16:39 +0200 Subject: [PATCH 0721/1172] include #1795 --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index bfb73bccb6..fea7c3746c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -23,7 +23,8 @@ feature + bugfix release SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) - added easyconfigs for 4 new software bundles: - R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) + R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), + R-bundle-pbd (#1659) - added easyconfigs for new GNU toolchain (#1346, #1669) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added example easyconfig for generating buildenv module (#1503) -- GitLab From b853f6a8c1796a3dc843cc33d2008cd53792a88b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:26:39 +0200 Subject: [PATCH 0722/1172] move up biomaRt and rtracklayer --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 4d63b897fb..e873d159b8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,6 +81,8 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), @@ -90,13 +92,11 @@ exts_list = [ ('NOISeq', '2.12.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), - ('biomaRt', '2.24.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), -- GitLab From a7f1c3703c59899b86f43d9015f94975c6f29943 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:28:13 +0200 Subject: [PATCH 0723/1172] drop duplicate samr --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index e873d159b8..03f3e4ca29 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -126,7 +126,6 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), - ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} -- GitLab From 162e94acb808417537a65209848ec586e8b9afef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:21:49 +0200 Subject: [PATCH 0724/1172] include GEOquery --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 03f3e4ca29..5b03ff4971 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -116,6 +116,7 @@ exts_list = [ ('KEGGREST', '1.8.0', bioconductor_options), ('KEGGgraph', '1.26.0', bioconductor_options), ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), -- GitLab From 60a1ef9f3066b1d0d056d31cfd93d8409aa336cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:29:07 +0200 Subject: [PATCH 0725/1172] add FDb.InfiniumMethylation.hg19 --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 5b03ff4971..3042f7627a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -118,6 +118,7 @@ exts_list = [ ('KEGGprofile', '1.10.0', bioconductor_options), ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), -- GitLab From 2557dc5f9d8a0b0c5870cf09eabe430f97499d24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:58:10 +0200 Subject: [PATCH 0726/1172] add missing R pkgs --- ...bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 14 ++++++++++---- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 12 +++++++++++- 2 files changed, 21 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 4d24094c6b..dcfb8699cb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -51,6 +51,9 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), @@ -70,12 +73,17 @@ exts_list = [ ('oligoClasses', '1.30.0', bioconductor_options), ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -84,14 +92,11 @@ exts_list = [ ('NOISeq', '2.12.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), - ('biomaRt', '2.24.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), @@ -111,7 +116,9 @@ exts_list = [ ('KEGGREST', '1.8.0', bioconductor_options), ('KEGGgraph', '1.26.0', bioconductor_options), ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), @@ -121,7 +128,6 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), - ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index e180920b15..37f178514d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -295,6 +295,11 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.29', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), @@ -327,6 +332,12 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('RCurl', '1.95-4.7', ext_options), ('httr', '0.6.1', ext_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), @@ -336,7 +347,6 @@ exts_list = [ ('spatstat', '1.41-1', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), - ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), ] -- GitLab From f88cc097dbcb4dae8f955222ea5f189cf8a969e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 20:17:35 +0200 Subject: [PATCH 0727/1172] bump release date --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index fea7c3746c..cfe294a3e1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 4,053 easyconfig files, for 673 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. -v2.2.0 (July 14th 2015) +v2.2.0 (July 15th 2015) ----------------------- feature + bugfix release -- GitLab From b69bfffcd363b1bccdac3a845fd9f13ce2fee00d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 20:25:54 +0200 Subject: [PATCH 0728/1172] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cfe294a3e1..8accdf9f3e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ 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 4,053 easyconfig files, for 673 different software packages, +The latest version of easybuild-easyconfig provides 4,061 easyconfig files, for 673 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.2.0 (July 15th 2015) -- GitLab From 0cd0cf1694fa8ea7003943505e93f699a7973d16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 09:06:40 +0200 Subject: [PATCH 0729/1172] revert #1785, patch is incomplete and causes segfaults --- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ---- .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 5 ----- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 4 ---- .../o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch | 9 --------- 27 files changed, 93 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 4ed82a3c67..d88a606fa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 8196616926..b42d9a8b03 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 765b625b39..fc479108fe 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 2dafe6d37c..8b588833b0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,10 +19,6 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index b52aee2a71..168f6f9d23 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 27fe1fb0fc..933369e32b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,10 +24,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 47f67c7470..ccbc9394ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index d4ff682eca..ce23f55355 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 7bf566224c..c6b40582c8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index ca196d7cca..2afbc4733e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 77911abd5d..8af372736a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index d4c15d5bf5..2ae7377c37 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index f23bde1400..4fc8978e4d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 403555039f..0bb4349893 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,10 +18,6 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 7ea527459f..e9f2f244ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 34b0c2b430..6687a0ffa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,10 +23,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index dc5a005db0..10774dff41 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-%(version)s_common-cuda-lib.patch', 'OpenMPI-%(version)s-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index e03880908d..eeb7c2fe82 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index f7b63ddff5..a47fa4f0f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index 713b0ea77b..c6c6f0c9ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,10 +20,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index 21b804f8c3..f5e9417cad 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} 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 @@ -22,10 +21,6 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 722d00ac9a..2eb439ac34 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index 97c6962989..e009a63259 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index 5f77464b2d..780c3c78ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,10 +22,6 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d9c37cd004..ca0afea9dc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,10 +23,6 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 06ce242b8b..095d22d991 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - 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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch deleted file mode 100644 index 0d7989a781..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch +++ /dev/null @@ -1,9 +0,0 @@ ---- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 -+++ opal/etc/openmpi-mca-params.conf 2015-06-08 10:36:05.387902000 +0200 -@@ -56,3 +56,6 @@ - - # See "ompi_info --param all all" for a full listing of Open MPI MCA - # parameters available and their default values. -+ -+# Fix bug in the initialization of the value when using the infiniband module. (ref: http://www.open-mpi.org/community/lists/users/2015/05/26913.php) -+btl_openib_memalign_threshold=12288 -- GitLab From f1d98f4c5567db9b007e9eda833b1506b4bd0b23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 09:46:07 +0200 Subject: [PATCH 0730/1172] remove PR #1785 from 2.2.0 release notes (see #1798) --- RELEASE_NOTES | 1 - 1 file changed, 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8accdf9f3e..84f7b36994 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -66,7 +66,6 @@ feature + bugfix release - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) - fix source_urls in netCDF easyconfigs (#1766) - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) - - add Infiniband-related patch for OpenMPI versions < 1.8.6 (#1785) v2.1.1 (May 18th 2015) ---------------------- -- GitLab From 5fae463072a3d30643290733969cb50d53b57559 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:10:32 +0200 Subject: [PATCH 0731/1172] fix typo --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 84f7b36994..7d3ae9ed16 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -49,7 +49,7 @@ feature + bugfix release - include Tcl and Tk as dependencies in R easyconfig (#1623) - add patch for installing paycheck as Py3 extension (#1629) - add Perl dependency in git 2.x easyconfigs (#1631) - - fix easycofnig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635) - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) -- GitLab From 1c10dae6d02c6f7625134fb29dd5d6ce4df6abe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:40:31 +0200 Subject: [PATCH 0732/1172] bump version to 2.3.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d9262a0b8c..d3563514ac 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0' +VERSION = '2.3.0dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c90a030836bd3dc09eef4e82047ede30d3f09fde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:40:42 +0200 Subject: [PATCH 0733/1172] {chem}[intel/2015a] ABINIT 7.10.4 using included deps (netCDF, libxc) --- .../ABINIT-7.10.4-intel-2015a-incl-deps.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb new file mode 100644 index 0000000000..a8aa421345 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' +versionsuffix = '-incl-deps' + +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': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' " +configopts += "--with-dft-flavor='atompaw+bigdft+libxc+wannier90' " +configopts += '--with-linalg-flavor=mkl --with-linalg-libs="-L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += '--enable-mpi=yes --with-mpi-level=2 --enable-mpi-io=yes ' +configopts += '--with-fft-flavor=fftw3-mkl --with-fft-libs="-L$FFT_LIB_DIR $LIBFFT" ' +configopts += '--with-fft-incs=-I$FFT_INC_DIR/fftw ' +configopts += '--enable-gw-dpc="yes" --enable-64bit-flags="yes" ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From fdd766bd19ec05bce3d89153e73011cf12476e1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 16:28:50 +0200 Subject: [PATCH 0734/1172] {tools}[dummy] EasyBuild 2.2.0 --- .../e/EasyBuild/EasyBuild-2.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb new file mode 100644 index 0000000000..116950af4b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.2.0' + +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-2.2.3.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 01c6a2b26229619769c78bd49afc69f20baebc68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jul 2015 09:13:30 +0200 Subject: [PATCH 0735/1172] bump version to 2.2.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d9262a0b8c..b752afaff7 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0' +VERSION = '2.2.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From e5c4b2b03017c1463b83449bf1b0a2673d507010 Mon Sep 17 00:00:00 2001 From: Kay Thust Date: Wed, 22 Jul 2015 14:33:14 +0200 Subject: [PATCH 0736/1172] this version does not work with the old patch --- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 24 ++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb new file mode 100644 index 0000000000..8b1426bc88 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -0,0 +1,24 @@ +name = 'tbb' +version = '4.3.6.211' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_%s_%s.tgz' % (name, version)] + +moduleclass = 'lib' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -- GitLab From e73ad9af2c0a1aa1ae447736f5159430109ac54f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 27 Jul 2015 12:50:08 +0200 Subject: [PATCH 0737/1172] Update molmod and matplotlib for Python 2.7.9 intel 2015a. --- ...tplotlib-1.2.1-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ .../molmod-1.0-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..959081d6a0 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': '2015a'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b6703cee30 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +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': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 1bb62994bcdb84401822125bfae0e9c839048e5c Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 27 Jul 2015 17:39:46 +0200 Subject: [PATCH 0738/1172] Update fastx-toolkit for newer intel compilers. --- .../FASTX-Toolkit-0.0.14-intel-2015a.eb | 45 +++++++++++++++++++ .../libgtextutils-0.6.1-intel-2015a.eb | 33 ++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb new file mode 100644 index 0000000000..13d9d1cb72 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -0,0 +1,45 @@ +## +# 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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +altname = name.lower().replace('-','_') +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['%s-%%(version)s.tar.bz2' % altname] + +dependencies = [('libgtextutils', '0.6.1')]; + +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' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb new file mode 100644 index 0000000000..3bb784683f --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.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:: 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 = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } + +moduleclass = 'bio' -- GitLab From 18e06c15ee1de5e40b63a5313ca10070b3613750 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 29 Jul 2015 17:15:49 +0200 Subject: [PATCH 0739/1172] Add libraries for Python which are used for IPython notebook. --- .../p/Python/Python-2.7.10-intel-2015a.eb | 24 +++++++++++++++++++ .../p/Python/Python-2.7.9-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 1977d33177..29266a2fa0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 2c04d1e9a7..8b74208902 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,6 +114,30 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' -- GitLab From 18eadb23badcc94f691b6e9dce75dc45bf80adad Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 30 Jul 2015 11:59:59 +0200 Subject: [PATCH 0740/1172] Add Bowtie2 intel 2015a version since it's used with FASTX. --- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb new file mode 100644 index 0000000000..cc4bd53b3a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.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: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +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': 'intel', 'version': '2015a'} + +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 a73906b6163fbdb7ac23acb06689d02c1413a6a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Aug 2015 08:42:17 +0200 Subject: [PATCH 0741/1172] {tools}[dummy] GC3Pie 2.4.1 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb new file mode 100644 index 0000000000..b62aa2387d --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.1' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 7c12d6eb928775a4c0cd859a1a025c8cca40b370 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 5 Aug 2015 10:38:52 +0200 Subject: [PATCH 0742/1172] fixes for mpi enabled h5py --- .../easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 44ec9edf7c..f4b587afd4 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -19,6 +19,9 @@ pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pyver) +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + dependencies = [ (python, pyver), ('HDF5', '1.8.14'), -- GitLab From 9d64e69db1d24bce2bfae252ea30630e19651d4b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 09:42:49 +0200 Subject: [PATCH 0743/1172] Add molmod for Python 2.7.10 --- ...plotlib-1.2.1-intel-2015a-Python-2.7.10.eb | 35 +++++++++++++++++++ .../molmod-1.0-intel-2015a-Python-2.7.10.eb | 34 ++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..080aad8636 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..5d19338ab3 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +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': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 7c6bfa870a65392249f8918d7c183ba8f5f6e48e Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 12:07:34 +0200 Subject: [PATCH 0744/1172] Whitespace changes. --- .../l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb index 3bb784683f..16d490f92b 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb @@ -18,7 +18,6 @@ version = '0.6.1' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" - toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,8 +25,8 @@ sources = [SOURCE_TAR_BZ2] source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { - 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], - 'dirs': ['lib/pkgconfig'] - } + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} moduleclass = 'bio' -- GitLab From 23520bf3812c985129de4c52a5d31a75a9b84bce Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 14:51:00 +0200 Subject: [PATCH 0745/1172] Add bowtie for intel 2015a. --- .../b/Bowtie/Bowtie-1.1.2-intel-2015a.eb | 30 +++++++++++++++++++ .../b/Bowtie/compiler-agnostic.patch | 14 +++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000..bbe3401bf5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -0,0 +1,30 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team +easyblock = 'MakeCp' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['compiler-agnostic.patch', 'int64typedef.patch'] + +files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bowtie', 'bin/bowtie-inspect'], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch new file mode 100644 index 0000000000..a6c59b8e2f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch @@ -0,0 +1,14 @@ +diff --git a/Makefile.orig b/Makefile +index aaccb8b..0e98c62 100644 +--- a/Makefile.orig ++++ b/Makefile +@@ -8,9 +8,6 @@ bindir = $(prefix)/bin + SEQAN_DIR = SeqAn-1.1 + SEQAN_INC = -I $(SEQAN_DIR) + INC = $(SEQAN_INC) -I third_party +-CPP = g++ +-CXX = $(CPP) +-CC = gcc + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 + BOWTIE_SHARED_MEM = 1 -- GitLab From 48d6f1e0f1fcc33308b2c3ed97515a19db3e734e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 10:36:14 +0200 Subject: [PATCH 0746/1172] {chem}[intel/2015a] libbeef 0.1.1 --- .../l/libbeef/libbeef-0.1.1-intel-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb new file mode 100644 index 0000000000..d5d17f503c --- /dev/null +++ b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libbeef' +version = '0.1.1' + +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' +description = """libbeef is a package providing the class of BEEF-vdW functionals and + Bayesian error estimates to Fortran- or C-based DFT codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476'] +sources = [SOURCE_TAR_GZ] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From aa90db067f20dcc928e5edde782985bb09445e21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 10:39:26 +0200 Subject: [PATCH 0747/1172] bump Bioconductor 3.1 package versions --- ...R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 12 ++++++------ .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index dcfb8699cb..cfe8ae2e84 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -42,13 +42,13 @@ bioconductor_options = { exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.5', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -59,11 +59,11 @@ exts_list = [ ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), @@ -97,11 +97,11 @@ exts_list = [ ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 3042f7627a..1f51e42d01 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -42,13 +42,13 @@ bioconductor_options = { exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.5', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -59,11 +59,11 @@ exts_list = [ ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), @@ -97,11 +97,11 @@ exts_list = [ ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), -- GitLab From 14915716988c7a898528eccc9e5eeb575fe69374 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 10:48:25 +0200 Subject: [PATCH 0748/1172] Use buildopts instead of patching the makefile. --- .../b/Bowtie/Bowtie-1.1.2-intel-2015a.eb | 4 +++- .../easyconfigs/b/Bowtie/compiler-agnostic.patch | 14 -------------- 2 files changed, 3 insertions(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb index bbe3401bf5..c3c415f11f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -17,7 +17,9 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] -patches = ['compiler-agnostic.patch', 'int64typedef.patch'] +patches = ['int64typedef.patch'] + +buildopts = 'CC="$CC" CXX="$CXX" CPP="$CXX"' files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] diff --git a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch deleted file mode 100644 index a6c59b8e2f..0000000000 --- a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/Makefile.orig b/Makefile -index aaccb8b..0e98c62 100644 ---- a/Makefile.orig -+++ b/Makefile -@@ -8,9 +8,6 @@ bindir = $(prefix)/bin - SEQAN_DIR = SeqAn-1.1 - SEQAN_INC = -I $(SEQAN_DIR) - INC = $(SEQAN_INC) -I third_party --CPP = g++ --CXX = $(CPP) --CC = gcc - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 1 -- GitLab From e5218465e93a8777b7d9d532b79cf7848ce12e42 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 12:12:50 +0200 Subject: [PATCH 0749/1172] Remove change from 2.7.9 and add it to the foss version. --- .../p/Python/Python-2.7.10-foss-2015a.eb | 24 +++++++++++++++++++ .../p/Python/Python-2.7.9-intel-2015a.eb | 24 ------------------- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index aa976378fe..466c60183d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 8b74208902..2c04d1e9a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,30 +114,6 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], - }), - ('Jinja2', '2.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('jsonpointer', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' -- GitLab From 1e3d5ae4324d43c05bca0c8ba595b16a8f8400c8 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 15:14:37 +0200 Subject: [PATCH 0750/1172] Update versions on @boegel's request. --- .../easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.10-intel-2015a.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 466c60183d..1d7d341095 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -119,22 +119,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.7.3', { + ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.7', { + ('jsonpointer', '1.9', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.4.0', { + ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-1', { + ('functools32', '3.2.3-2', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.5.1', { + ('mistune', '0.7', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.1', { + ('tornado', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 29266a2fa0..a808b9876c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -119,22 +119,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.7.3', { + ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.7', { + ('jsonpointer', '1.9', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.4.0', { + ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-1', { + ('functools32', '3.2.3-2', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.5.1', { + ('mistune', '0.7', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.1', { + ('tornado', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { -- GitLab From 8d2631610549866bbb93896893fb7b96cd1cae1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 15:50:34 +0200 Subject: [PATCH 0751/1172] style fixes in PCRE and XZ easyconfigs --- .../p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb | 9 ++++----- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb | 10 ++++------ easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb | 10 ++++------ easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb | 6 ++---- easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb | 10 ++++------ easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb | 5 ++++- 12 files changed, 46 insertions(+), 49 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb index e95902eec8..4a9ef5925f 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb index 0f58883e8e..5916d698fc 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb index ae806687ed..e5f29eb85e 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb index 0a2a528704..871d373c07 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb @@ -4,16 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" - +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': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb index 82e14a704f..365ae1e42a 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.12' 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. -""" +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': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb index fd30422f0b..a4df16eaad 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.35' 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. -""" +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': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index dd7d330b7c..7881c04da4 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -4,10 +4,8 @@ name = 'PCRE' version = '8.36' 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. -""" +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': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb index 64ff0ffd54..f2529df084 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.36' 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. -""" +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': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb index fad6a95d95..3d54b29efd 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb index 171e02c46b..e60568da6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb @@ -6,12 +6,13 @@ version = '5.0.5' 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/'] -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb index c7b1752259..6f7148a406 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb @@ -6,12 +6,13 @@ version = '5.0.5' 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/'] -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb index 5a6ed9b122..99b4d29f28 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb @@ -6,10 +6,13 @@ version = '5.2.0' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], -- GitLab From fd12b56c77004c7adf0d0e3f6a088ee94b74c264 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 23:52:15 +0200 Subject: [PATCH 0752/1172] {tools}[dummy] GC3Pie 2.4.2 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb new file mode 100644 index 0000000000..e73e2257cc --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.2' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 5a45e61862b71a718c6f16aff446dc00b04ad50b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 7 Aug 2015 10:03:08 +0200 Subject: [PATCH 0753/1172] correct import of fancylogger --- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9ccac83960..68fd8a7c50 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -36,7 +36,7 @@ import shutil import sys import tempfile from distutils.version import LooseVersion -from vsc import fancylogger +from vsc.utils import fancylogger from vsc.utils.missing import nub from unittest import TestCase, TestLoader, main diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 65497da038..6afbd6ffb1 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,7 +36,8 @@ import shutil import sys import tempfile import unittest -from vsc import fancylogger + +from vsc.utils import fancylogger import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e -- GitLab From ca880b15a9fcf87db803cf8b1a15d8baf162e585 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 00:20:04 +0200 Subject: [PATCH 0754/1172] put dummy template values in place to make comparison with dumped easyconfig more robust --- .../easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- test/easyconfigs/easyconfigs.py | 8 ++++++++ 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb index 0e1e6d0fb4..67920d1a2d 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb index 5fb2a1352d..b7b0c00339 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 50633eb598..7bcbad6706 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -30,7 +30,7 @@ dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] cmds_map = [ - ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o fastqz'), + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') ] diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 68fd8a7c50..a8b8f5a2f2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -311,6 +311,14 @@ def template_easyconfig_test(self, spec): dumped_ec = EasyConfig(test_ecfile) os.remove(test_ecfile) + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + } + ec.template_values.update(dummy_template_values) + dumped_ec.template_values.update(dummy_template_values) + for key in sorted(ec._config): self.assertEqual(ec[key], dumped_ec[key]) -- GitLab From 16da5970c776b1e545d6927f25d39b950fee28bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 11:38:55 +0200 Subject: [PATCH 0755/1172] {toolchain} GNU 4.9.3-2.25 --- .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 37 +++++++++++++++ .../g/GCC/GCC-4.9.3-binutils-2.25.eb | 45 +++++++++++++++++++ easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb | 20 +++++++++ .../zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb | 24 ++++++++++ 4 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb 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 new file mode 100644 index 0000000000..d964881000 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + # 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 +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/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..6b122513e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,45 @@ +name = "GCC" +version = '4.9.3' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': ''} + +mpfr_version = '3.1.2' + +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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.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' diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..e9a60222d5 --- /dev/null +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'GNU' +gccver = '4.9.3' +binutilsver = '2.25' +version = '%s-%s' % (gccver, binutilsver) + +homepage = 'http://www.gnu.org/software/' +description = "Compiler-only toolchain with GCC and binutils." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # GCC built on top of (dummy-built) binutils + ('GCC', gccver, '-binutils-%s' % binutilsver), + # binutils built on top of GCC, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCC', '%s-binutils-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..dc4517d950 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,24 @@ +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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 8cebbae96a95eef246c41c1729df0dc6ad106f33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 11:45:38 +0200 Subject: [PATCH 0756/1172] {devel}[GNU-4.9.3-2.25] Autotools 20150215 --- .../Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb | 26 +++++++++++++++ .../Automake/Automake-1.15-GNU-4.9.3-2.25.eb | 33 +++++++++++++++++++ .../Autotools-20150215-GNU-4.9.3-2.25.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb | 17 ++++++++++ .../m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb | 23 +++++++++++++ 5 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..90bf6609a6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..1c089451d8 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..80fa06d91b --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..99efd1e796 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..ad83091b2b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b3b0981ff942f046bd421acbebb829245de412c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 11:49:36 +0200 Subject: [PATCH 0757/1172] switch to GCC 4.9.3 + GNU 4.9.3-2.25 --- easybuild/easyconfigs/g/gompi/gompi-2015b.eb | 2 +- ...-1.11.0-GNU-5.1.0-2.25.eb => hwloc-1.11.0-GNU-4.9.3-2.25.eb} | 2 +- ....0.10-GNU-5.1.0-2.25.eb => numactl-2.0.10-GNU-4.9.3-2.25.eb} | 2 +- ...-1.8.6-GNU-5.1.0-2.25.eb => OpenMPI-1.8.6-GNU-4.9.3-2.25.eb} | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.11.0-GNU-5.1.0-2.25.eb => hwloc-1.11.0-GNU-4.9.3-2.25.eb} (94%) rename easybuild/easyconfigs/n/numactl/{numactl-2.0.10-GNU-5.1.0-2.25.eb => numactl-2.0.10-GNU-4.9.3-2.25.eb} (94%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-1.8.6-GNU-5.1.0-2.25.eb => OpenMPI-1.8.6-GNU-4.9.3-2.25.eb} (95%) diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb index 0679b7fad6..50c6861981 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -9,7 +9,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '5.1.0' +gccver = '4.9.3' binutilsver = '2.25' tcver = '%s-binutils-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb similarity index 94% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb index 71b80ef6aa..086602c3aa 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb @@ -11,7 +11,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide 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': 'GNU', 'version': '5.1.0-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [('numactl', '2.0.10')] diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb similarity index 94% rename from easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb index 7f1c8eefc3..04cd4b9e23 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb @@ -10,7 +10,7 @@ description = """The numactl program allows you to run your application program 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': 'GNU', 'version': '5.1.0-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb index c54ad5d8b7..3e69e3901f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '1.8.6' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" -toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -- GitLab From 8941cac16506aac0b165cc6bd25015e06a3d4ef1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 11:51:45 +0200 Subject: [PATCH 0758/1172] switch to GCC 4.9.3 + GNU 4.9.3-2.25 --- easybuild/easyconfigs/f/foss/foss-2015b.eb | 2 +- ...-3.5.0.eb => OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb} | 2 +- .../ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb => OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb} (96%) diff --git a/easybuild/easyconfigs/f/foss/foss-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb index 2bb9b25e02..e8c588da67 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -9,7 +9,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, includi toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '5.1.0' +gccver = '4.9.3' binutilsver = '2.25' tcver = '%s-binutils-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index a7c27b0146..b11768a150 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -9,7 +9,7 @@ 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': 'GNU', 'version': '5.1.0-2.25'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb index 04520881ee..758c146b83 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -17,7 +17,7 @@ blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('GNU', '5.1.0-2.25'))] +dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.3-2.25'))] ## parallel build tends to fail, so disabling it parallel = 1 -- GitLab From 289bb67fe4d6c52b54a19255f148c99c1745740e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 11:55:11 +0200 Subject: [PATCH 0759/1172] switch to GNU 4.9.3-2.25 --- ...3.187-GNU-5.1.0-2.25.eb => icc-2015.3.187-GNU-4.9.3-2.25.eb} | 2 +- ...-GNU-5.1.0-2.25.eb => iccifort-2015.3.187-GNU-4.9.3-2.25.eb} | 2 +- ...187-GNU-5.1.0-2.25.eb => ifort-2015.3.187-GNU-4.9.3-2.25.eb} | 2 +- ...pi-7.3.5-GNU-5.1.0-2.25.eb => iimpi-7.3.5-GNU-4.9.3-2.25.eb} | 2 +- ....0-2.25.eb => imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb} | 2 +- ....eb => impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb} | 2 +- easybuild/easyconfigs/i/intel/intel-2015b.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/i/icc/{icc-2015.3.187-GNU-5.1.0-2.25.eb => icc-2015.3.187-GNU-4.9.3-2.25.eb} (95%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2015.3.187-GNU-5.1.0-2.25.eb => iccifort-2015.3.187-GNU-4.9.3-2.25.eb} (91%) rename easybuild/easyconfigs/i/ifort/{ifort-2015.3.187-GNU-5.1.0-2.25.eb => ifort-2015.3.187-GNU-4.9.3-2.25.eb} (95%) rename easybuild/easyconfigs/i/iimpi/{iimpi-7.3.5-GNU-5.1.0-2.25.eb => iimpi-7.3.5-GNU-4.9.3-2.25.eb} (93%) rename easybuild/easyconfigs/i/imkl/{imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb => imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb} (90%) rename easybuild/easyconfigs/i/impi/{impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb => impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb} (88%) diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index ab75663608..aca2626f97 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%(version)s.tgz'] gnu = 'GNU' -gnuver = '5.1.0-2.25' +gnuver = '4.9.3-2.25' versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb similarity index 91% rename from easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 91b5c21fb3..58c54bd7ef 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -2,7 +2,7 @@ easyblock = "Toolchain" name = 'iccifort' version = '2015.3.187' -versionsuffix = '-GNU-5.1.0-2.25' +versionsuffix = '-GNU-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index 5f9e537efe..f944202e89 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%(version)s.tgz'] gnu = 'GNU' -gnuver = '5.1.0-2.25' +gnuver = '4.9.3-2.25' versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb similarity index 93% rename from easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb index 5ddcd4cb45..9b59992b23 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -2,7 +2,7 @@ easyblock = "Toolchain" name = 'iimpi' version = '7.3.5' -versionsuffix = '-GNU-5.1.0-2.25' +versionsuffix = '-GNU-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb similarity index 90% rename from easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb index 60bd4ce3a2..b76de536ee 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, 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': '7.3.5-GNU-5.1.0-2.25'} +toolchain = {'name': 'iimpi', 'version': '7.3.5-GNU-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb similarity index 88% rename from easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb rename to easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 8c0670293a..0cc5dc235f 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -6,7 +6,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag 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': '2015.3.187-GNU-5.1.0-2.25'} +toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb index 8ac5d4eba1..e0b4b71ab1 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -9,7 +9,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2015.3.187' -gccsuff = '-GNU-5.1.0-2.25' +gccsuff = '-GNU-4.9.3-2.25' dependencies = [ ('icc', compver, gccsuff), -- GitLab From d151b46d3251dc5ae8099ee3ec787c8e02714a34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 12:00:11 +0200 Subject: [PATCH 0760/1172] fix MPFR patch used in easyconfig for GCC 4.9.3 on top of binutils 2.25 --- easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb index 6b122513e5..d762426d06 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -27,7 +27,7 @@ sources = [ builddependencies = [('binutils', binutilsver)] -patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.tar.bz2 -- GitLab From c424d2f5195b43e1e60b33f25295a9f895f6847a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 21:28:51 +0200 Subject: [PATCH 0761/1172] {compiler}[dummy] GCC 5.2.0 --- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 49 + .../GCC/mpfr-3.1.3-allpatches-20150717.patch | 1699 +++++++++++++++++ 2 files changed, 1748 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb new file mode 100644 index 0000000000..c25b63f7b1 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -0,0 +1,49 @@ +name = 'GCC' +version = '5.2.0' + +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 = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20150717.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'a51bcfeb3da7dd4c623e27207ed43467', # gcc-5.2.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.l.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + 'e502185ebb22b41c528f183bb22a7569', # mpfr-3.1.3-allpatches-20150717.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/GCC/mpfr-3.1.3-allpatches-20150717.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch new file mode 100644 index 0000000000..7793316052 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch @@ -0,0 +1,1699 @@ +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 (" Date: Tue, 11 Aug 2015 11:59:16 +0200 Subject: [PATCH 0762/1172] bump AFNI version + fiddle with dep versions to resolve conflicts --- ...-2015a.eb => AFNI-20150717-intel-2015a.eb} | 14 +++---- .../t/tcsh/tcsh-6.19.00-intel-2015a.eb | 38 +++++++++++++++++++ 2 files changed, 45 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/a/AFNI/{AFNI-20141023-intel-2015a.eb => AFNI-20150717-intel-2015a.eb} (88%) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb similarity index 88% rename from easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb rename to easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 94ac7b95ff..5d47f1566c 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20141023-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'AFNI' -version = '20141023' +version = '20150717' homepage = 'http://afni.nimh.nih.gov/' description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - @@ -14,7 +14,7 @@ toolchainopts = {'openmp': True, 'pic': True} # detailed release notes are available at http://afni.nimh.nih.gov/pub/dist/doc/misc/history/afni_hist_level1_all.html # but last update doesn't match datestamp of most recent afni_src.tgz? sources = ['afni_src-%(version)s.tgz'] -checksums = ['87d8fcea9b9214dd37f5d89d61605647'] +checksums = ['985ce725a68c7b498e3402fd52b41811'] patches = ['AFNI-%(version)s_omp-pragma-statement-fix.patch'] @@ -23,19 +23,19 @@ libx11suff = '-libX11-1.6.3' pyver = '2.7.9' majpyver = '.'.join(pyver.split('.')[:2]) dependencies = [ - ('tcsh', '6.18.01'), + ('tcsh', '6.19.00'), ('libXp', '1.0.3'), ('libXt', '1.1.4', libx11suff), ('libXpm', '3.5.11'), ('libXmu', '1.1.2', libx11suff), ('motif', '2.3.4', libx11suff), - ('R', '3.1.3'), - ('PyQt', '4.11.3', '-Python-%s' % pyver), + ('R', '3.1.2'), + ('PyQt', '4.11.4', '-Python-%s' % pyver), ('expat', '2.1.0'), - ('libpng', '1.6.16'), + ('libpng', '1.6.18'), ('libjpeg-turbo', '1.4.0'), ('GSL', '1.16'), - ('GLib', '2.44.0', '', ('GCC', '4.9.2')), + ('GLib', '2.40.0'), # must match version used in Qt (via PyQt) ] buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb new file mode 100644 index 0000000000..ef7cef982f --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 272443675041f0789e2fee39315aaeea5a1d005d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Aug 2015 12:04:05 +0200 Subject: [PATCH 0763/1172] Update texinfo-5.2-GCC-4.8.2.eb Added dependency on texlive. Completed the build process to make necessary installations in custom ```TEXMFHOME``` and have module set that variable. This should only really be used as a build dependency since it will overwrite any default/user value for ```TEXMFHOME``` --- .../easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 233c5a0e62..6959a7d7b8 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -1,8 +1,3 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -## - easyblock = 'ConfigureMake' name = 'texinfo' @@ -16,6 +11,14 @@ sources = [SOURCELOWER_TAR_XZ] toolchain = {'name': 'GCC', 'version': '4.8.2'} +osdependencies = ['texlive'] + +preinstallopts = "mkdir -p %(installdir)s/texmf/{doc,tex}/{context,eplain,generic,latex,lualatex,plain,xelatex,xetex} && " +preinstallopts += "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users TEXMFHOME so this module should only really be used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} + sanity_check_paths = { 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], 'dirs': [], -- GitLab From 76234bc6cbb1b8f9ef747aa763f7dc91e4ce8c7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 12:15:25 +0200 Subject: [PATCH 0764/1172] fix filename for AFNI patch --- ...NI-20141023_omp-pragma-statement-fix.patch | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch b/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch deleted file mode 100644 index 7f3c8a8c07..0000000000 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20141023_omp-pragma-statement-fix.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff -ru afni_src.orig/thd_dset_to_vectim.c afni_src/thd_dset_to_vectim.c ---- afni_src.orig/thd_dset_to_vectim.c 2015-04-02 02:35:57.000000000 +0200 -+++ afni_src/thd_dset_to_vectim.c 2015-04-03 17:08:33.340433024 +0200 -@@ -74,8 +74,9 @@ - - if( ignore > 0 ){ /* extract 1 at a time, save what we want */ - -+ float *var; - #pragma omp critical (MALLOC) -- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; -+ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; - for( kk=iv=0 ; iv < nvox ; iv++ ){ - if( mmm[iv] == 0 ) continue ; - (void)THD_extract_array( iv , dset , 0 , var ) ; -@@ -296,8 +297,9 @@ - - if( nvals < DSET_NVALS(dset) ){ /* extract 1 at a time, save what we want */ - -+ float *var; - #pragma omp critical (MALLOC) -- float *var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; -+ var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; - for( kk=iv=0 ; iv < nvox ; iv++ ){ - if( mmm[iv] == 0 ) continue ; - (void)THD_extract_array( iv , dset , 0 , var ) ; -@@ -463,8 +465,9 @@ - - if( ignore > 0 ){ /* extract 1 at a time, save what we want */ - -+ float *var; - #pragma omp critical (MALLOC) -- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; -+ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; - mmmt = mmmv[0]; - for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){ - if( mmmt[iv] == 0 ) continue ; -- GitLab From ee708bfa16087fda449e13f308e52dcabe197cc0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 12:27:44 +0200 Subject: [PATCH 0765/1172] use OpenMPI 1.8.8 in gompi/2015b --- easybuild/easyconfigs/g/gompi/gompi-2015b.eb | 2 +- .../o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb index 50c6861981..dd242ab254 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -17,7 +17,7 @@ tcver = '%s-binutils-%s' % (gccver, binutilsver) dependencies = [ ('GCC', gccver, '-binutils-%s' % binutilsver), ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.6', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + ('OpenMPI', '1.8.8', '', ('GNU', '%s-%s' % (gccver, binutilsver))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..5206425bdf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.8' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.0')] + +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' -- GitLab From 2a9564814f59dbc3e728f9294475d6130cc52f89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 12:46:10 +0200 Subject: [PATCH 0766/1172] really fix filename for AFNI patch --- ...NI-20150717_omp-pragma-statement-fix.patch | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch b/easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch new file mode 100644 index 0000000000..7f3c8a8c07 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch @@ -0,0 +1,36 @@ +diff -ru afni_src.orig/thd_dset_to_vectim.c afni_src/thd_dset_to_vectim.c +--- afni_src.orig/thd_dset_to_vectim.c 2015-04-02 02:35:57.000000000 +0200 ++++ afni_src/thd_dset_to_vectim.c 2015-04-03 17:08:33.340433024 +0200 +@@ -74,8 +74,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -296,8 +297,9 @@ + + if( nvals < DSET_NVALS(dset) ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; ++ var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -463,8 +465,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + mmmt = mmmv[0]; + for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){ + if( mmmt[iv] == 0 ) continue ; -- GitLab From ef0830cffa3614592d545a03c4dfe605681a14d0 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Aug 2015 13:04:40 +0200 Subject: [PATCH 0767/1172] Update texinfo-5.2-GCC-4.8.2.eb Add a module load warning and remove unnecessary mkdir preinstallopt --- .../easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 6959a7d7b8..5cfe64489d 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -13,11 +13,15 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} osdependencies = ['texlive'] -preinstallopts = "mkdir -p %(installdir)s/texmf/{doc,tex}/{context,eplain,generic,latex,lualatex,plain,xelatex,xetex} && " -preinstallopts += "make TEXMF=%(installdir)s/texmf install-tex && " +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " -# This will overwrite a users TEXMFHOME so this module should only really be used as a build dependency +# This will overwrite a users TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = """\\n\\nThis module will set/overwrite any existing value for the environment variable TEXMFHOME.""" +modloadmsg += """\\nIf you use a custom texmf directory (such as \~/texmf) then you should copy files found in the""" +modloadmsg += """\\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" +modloadmsg += """\\n\\tcp -r \$TEXMFHOME /path/to/your/texmf/..""" +modloadmsg += """\\n\\texport TEXMFHOME=/path/to/your/texmf\\n\\n""" sanity_check_paths = { 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], -- GitLab From c009b556ef6531b854d588a3c72bcb93ef6bb772 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Aug 2015 13:09:59 +0200 Subject: [PATCH 0768/1172] Update texinfo-5.2-GCC-4.8.2.eb --- easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 5cfe64489d..19a557190b 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -17,7 +17,7 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = """\\n\\nThis module will set/overwrite any existing value for the environment variable TEXMFHOME.""" +modloadmsg = """\\n\\nThis module will set/overwrite the value for the environment variable TEXMFHOME.""" modloadmsg += """\\nIf you use a custom texmf directory (such as \~/texmf) then you should copy files found in the""" modloadmsg += """\\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" modloadmsg += """\\n\\tcp -r \$TEXMFHOME /path/to/your/texmf/..""" -- GitLab From 2f5c906f1bd22182fad2a9d29adf6e016bd205ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 13:29:51 +0200 Subject: [PATCH 0769/1172] bump OpenMPI version to 1.8.8 in foss/2015b --- easybuild/easyconfigs/f/foss/foss-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb index e8c588da67..b30caf2279 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -30,7 +30,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) dependencies = [ ('GCC', gccver, '-binutils-%s' % binutilsver), ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.6', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + ('OpenMPI', '1.8.8', '', ('GNU', '%s-%s' % (gccver, binutilsver))), (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From 2ecdffa9ca5b308c4d9888028d06c748fc8b6f1a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Aug 2015 13:31:55 +0200 Subject: [PATCH 0770/1172] Update texinfo-5.2-GCC-4.8.2.eb No need to escape anything --- .../easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 19a557190b..9772c601e3 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -17,11 +17,11 @@ preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " # This will overwrite a users TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = """\\n\\nThis module will set/overwrite the value for the environment variable TEXMFHOME.""" -modloadmsg += """\\nIf you use a custom texmf directory (such as \~/texmf) then you should copy files found in the""" -modloadmsg += """\\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" -modloadmsg += """\\n\\tcp -r \$TEXMFHOME /path/to/your/texmf/..""" -modloadmsg += """\\n\\texport TEXMFHOME=/path/to/your/texmf\\n\\n""" +modloadmsg = """\n\nThis module will set/overwrite the value for the environment variable TEXMFHOME.""" +modloadmsg += """\nIf you use a custom texmf directory (such as ~/texmf) then you should copy files found in the""" +modloadmsg += """\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" +modloadmsg += """\n\tcp -r $TEXMFHOME /path/to/your/texmf/..""" +modloadmsg += """\n\texport TEXMFHOME=/path/to/your/texmf\n\n""" sanity_check_paths = { 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], -- GitLab From 5c0deef6ced52f6ddee80315ab0f6817e27db703 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Aug 2015 13:33:38 +0200 Subject: [PATCH 0771/1172] Update texinfo-5.2-GCC-4.8.2.eb --- easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 9772c601e3..ed8b3f6100 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -20,7 +20,7 @@ modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} modloadmsg = """\n\nThis module will set/overwrite the value for the environment variable TEXMFHOME.""" modloadmsg += """\nIf you use a custom texmf directory (such as ~/texmf) then you should copy files found in the""" modloadmsg += """\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" -modloadmsg += """\n\tcp -r $TEXMFHOME /path/to/your/texmf/..""" +modloadmsg += """\n\tcp -r $TEXMFHOME/* /path/to/your/texmf""" modloadmsg += """\n\texport TEXMFHOME=/path/to/your/texmf\n\n""" sanity_check_paths = { -- GitLab From bdd42a1b0b492cb65a18759cdf6e857c1f0bef63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 13:34:24 +0200 Subject: [PATCH 0772/1172] stick with libpng 1.6.16 (required by R 3.1.2) in AFNI easyconfig --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 5d47f1566c..a1bc13fc57 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -32,7 +32,7 @@ dependencies = [ ('R', '3.1.2'), ('PyQt', '4.11.4', '-Python-%s' % pyver), ('expat', '2.1.0'), - ('libpng', '1.6.18'), + ('libpng', '1.6.16'), ('libjpeg-turbo', '1.4.0'), ('GSL', '1.16'), ('GLib', '2.40.0'), # must match version used in Qt (via PyQt) -- GitLab From a15957cdc76281d459f98f156d70906b80bac6ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Aug 2015 18:26:42 +0200 Subject: [PATCH 0773/1172] style fixes in modloadmsg for texinfo --- .../easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index ed8b3f6100..11db942e72 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -15,13 +15,13 @@ osdependencies = ['texlive'] preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " -# This will overwrite a users TEXMFHOME so this module is best used as a build dependency +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} -modloadmsg = """\n\nThis module will set/overwrite the value for the environment variable TEXMFHOME.""" -modloadmsg += """\nIf you use a custom texmf directory (such as ~/texmf) then you should copy files found in the""" -modloadmsg += """\nnew TEXMFHOME to your custom directory and reset the value of TEXMFHOME to point to that space:""" -modloadmsg += """\n\tcp -r $TEXMFHOME/* /path/to/your/texmf""" -modloadmsg += """\n\texport TEXMFHOME=/path/to/your/texmf\n\n""" +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" sanity_check_paths = { 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], -- GitLab From 7489172a48f240698853bb3d977d55c8a681d4b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Aug 2015 11:59:06 +0200 Subject: [PATCH 0774/1172] sync up easyconfig for Python 2.7.10 with foss/2015b w.r.t. exts_list --- .../p/Python/Python-2.7.10-foss-2015b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 8d705315cc..87c42e20b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('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'], + }), + ('jsonpointer', '1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' -- GitLab From 98aba288fd622c4aaf0797ad28e0247d4665163c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Aug 2015 11:59:47 +0200 Subject: [PATCH 0775/1172] sync up easyconfig for Python 2.7.10 with intel/2015b w.r.t. exts_list --- .../p/Python/Python-2.7.10-intel-2015b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index a5115dc2be..58596bda71 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('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'], + }), + ('jsonpointer', '1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' -- GitLab From 4ab27ee7fa43d50a87c18074375eaf318d7b0f18 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 12 Aug 2015 12:29:09 +0200 Subject: [PATCH 0776/1172] Update texinfo-5.2-GCC-4.8.2.eb Add another sanity check file --- easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 11db942e72..7e2b9ee6aa 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -24,7 +24,7 @@ modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" sanity_check_paths = { - 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], + 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], 'dirs': [], } -- GitLab From bac448e4ea9c6e1820cffc7b60d8d6bd634d0939 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 09:44:59 +0100 Subject: [PATCH 0777/1172] Update IRanges to 2.2.7 for Bioconductor bundle --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index cfe8ae2e84..8b0b267981 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -43,7 +43,7 @@ exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), ('S4Vectors', '0.6.3', bioconductor_options), - ('IRanges', '2.2.5', bioconductor_options), + ('IRanges', '2.2.7', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 1f51e42d01..c0181513c0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -43,7 +43,7 @@ exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), ('S4Vectors', '0.6.3', bioconductor_options), - ('IRanges', '2.2.5', bioconductor_options), + ('IRanges', '2.2.7', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), -- GitLab From 39344ec4e822bad1ba998250c4fca5f5b1f35466 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 14:21:50 +0100 Subject: [PATCH 0778/1172] Update BiocParallel to 1.2.20 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 4 ++-- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index cfe8ae2e84..aa69363acd 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -48,13 +48,13 @@ exts_list = [ ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.2', bioconductor_options), + ('Biostrings', '2.36.3', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.2.9', bioconductor_options), + ('BiocParallel', '1.2.20', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 1f51e42d01..b3cd385d5c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -54,7 +54,7 @@ exts_list = [ ('lambda.r', '1.1.7', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), - ('BiocParallel', '1.2.9', bioconductor_options), + ('BiocParallel', '1.2.20', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), -- GitLab From b2404869b35bc00cffcf4e993c2fa8e36070c530 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 14:42:57 +0100 Subject: [PATCH 0779/1172] Update limma to 3.24.15 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index aa69363acd..ce14cd8362 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -63,7 +63,7 @@ exts_list = [ ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.14', bioconductor_options), + ('limma', '3.24.15', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index b3cd385d5c..4c3ef941fd 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -63,7 +63,7 @@ exts_list = [ ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.14', bioconductor_options), + ('limma', '3.24.15', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), -- GitLab From b2f59738edb0e0763c8a5c664819addc676f5ff2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 14:49:48 +0100 Subject: [PATCH 0780/1172] Update rtracklayer to 1.18.7 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index ce14cd8362..dd0457d542 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -81,7 +81,7 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), + ('rtracklayer', '1.28.7', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 4c3ef941fd..5acd5d2e3e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,7 +81,7 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), + ('rtracklayer', '1.28.7', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), -- GitLab From d880b639bacd2d63fcb6dbd487b6096c2e693c58 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 14:53:43 +0100 Subject: [PATCH 0781/1172] Update NOISeq to 2.14.0 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index dd0457d542..1b28219bd0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -89,7 +89,7 @@ exts_list = [ ('siggenes', '1.42.0', bioconductor_options), ('DynDoc', '1.46.0', bioconductor_options), ('genoset', '1.22.0', bioconductor_options), - ('NOISeq', '2.12.0', bioconductor_options), + ('NOISeq', '2.14.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 5acd5d2e3e..b311af6940 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -89,7 +89,7 @@ exts_list = [ ('siggenes', '1.42.0', bioconductor_options), ('DynDoc', '1.46.0', bioconductor_options), ('genoset', '1.22.0', bioconductor_options), - ('NOISeq', '2.12.0', bioconductor_options), + ('NOISeq', '2.14.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), -- GitLab From b1226e5cd92552419e08e3228716275e60eecc09 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Aug 2015 15:23:03 +0100 Subject: [PATCH 0782/1172] Update VariantAnnotation to 1.14.10 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 1b28219bd0..1f8de4dc60 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -98,7 +98,7 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('BSgenome', '1.36.3', bioconductor_options), - ('VariantAnnotation', '1.14.6', bioconductor_options), + ('VariantAnnotation', '1.14.10', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.1', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index b311af6940..51ca069167 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -98,7 +98,7 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('BSgenome', '1.36.3', bioconductor_options), - ('VariantAnnotation', '1.14.6', bioconductor_options), + ('VariantAnnotation', '1.14.10', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.1', bioconductor_options), -- GitLab From 4c02e45f07a2abc9b0d9cd0175ecbdbf42d3135a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 08:41:34 +0200 Subject: [PATCH 0783/1172] stop using 'unresolved_deps' in easyconfigs unit tests --- test/easyconfigs/easyconfigs.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a8b8f5a2f2..b8219c692d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -109,9 +109,6 @@ class EasyConfigTest(TestCase): for dep in ec['dependencies'][:]: if dep.get('external_module', False): ec['dependencies'].remove(dep) - for dep in ec['unresolved_deps'][:]: - if dep.get('external_module', False): - ec['unresolved_deps'].remove(dep) self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) @@ -152,7 +149,7 @@ class EasyConfigTest(TestCase): depmap = {} for spec in self.ordered_specs: build_deps = map(mk_dep_mod_name, spec['builddependencies']) - deps = map(mk_dep_mod_name, spec['unresolved_deps']) + deps = map(mk_dep_mod_name, spec['dependencies']) # 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)) -- GitLab From 3a4a6cb55c1a7a4b206b9e2e7e8c8f4e469f22c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 10:15:47 +0200 Subject: [PATCH 0784/1172] {devel}[intel/2015a] Boost 1.59.0 --- .../Boost-1.59.0-intel-2015a-Python-2.7.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..bdadbc8ed1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3449027d78943541bc6489597dd331cae2591878 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 10:17:20 +0200 Subject: [PATCH 0785/1172] {chem}[intel/2015a] PSI 4.0b5 w/ higher max. angular momentum + Python 2.7.10, Boost 1.59.0 --- ...0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb new file mode 100644 index 0000000000..cf5eb269ab --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb @@ -0,0 +1,38 @@ +name = 'PSI' +version = '4.0b5' +# 'maxam8': maximum angular momentum increased to 8 via LIBINT_NEW_AM +versionsuffix = '-mt-maxam8' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +# not using MPI results in a build relying on multithreaded BLAS solely +toolchainopts = {'usempi': False} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit + 'PSI-4.0b5-thread-pool.patch', + 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used +] + +python = 'Python' +pyver = '2.7.10' +pysuff = '-%s-%s' % (python, pyver) +versionsuffix += pysuff + +dependencies = [ + (python, pyver), + ('Boost', '1.59.0', pysuff), +] + +# increase maximum angular momentum to 8 (specified value has to be double of the intended max!) +configopts = '-DLIBINT_NEW_AM=16' + +moduleclass = 'chem' -- GitLab From 7e11a0167e6442d5b7e1d7540ca5b4dcc6722048 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Aug 2015 09:42:05 +0100 Subject: [PATCH 0786/1172] Update GATK to use Java 1.7.0_80 --- .../g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..f53b54862b --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# 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 = 'Tarball' + +name = 'GATK' +version = '3.3-0' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From b67eba3a544f4af05148405aa93a8cd000d35b98 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Aug 2015 09:46:37 +0100 Subject: [PATCH 0787/1172] Add version of picard with Java 1.7.0_80 --- .../p/picard/picard-1.119-Java-1.7.0_80.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb new file mode 100644 index 0000000000..e4658e7c57 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.119' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +moduleclass = 'bio' -- GitLab From 831c6fd209c8474bda94dae94456e60e305af692 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 11:24:31 +0200 Subject: [PATCH 0788/1172] add GMP as missing dep in Python 2.7.10 easyconfigs (required for pycrypto extension) --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 1 + easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 1d7d341095..39e03ec1d8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -22,6 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index a808b9876c..3ada190dc7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -22,6 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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 3b6e3db531bbe17c11d719127ac698057ebff0eb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Aug 2015 10:35:58 +0100 Subject: [PATCH 0789/1172] Use versionsuffix for Java dependency --- easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb index e4658e7c57..a097dca76d 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb @@ -9,6 +9,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] -dependencies = [('Java', '1.7.0_80')] +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] moduleclass = 'bio' -- GitLab From 17ebf421f69d81013eff85ec88641864429ace91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 11:50:25 +0200 Subject: [PATCH 0790/1172] {tools}[intel/2015a] pycosat 0.6.0 w/ Python 2.7.10 --- ...pycosat-0.6.0-intel-2015a-Python-2.7.10.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..a09ace02c0 --- /dev/null +++ b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pycosat' +version = '0.6.0' + +homepage = 'https://pypi.python.org/pypi/pycosat' +description = """pycosat provides efficient Python bindings to picosat on the C level, i.e. when importing pycosat, + the picosat solver becomes part of the Python process itself.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' -- GitLab From 0e76c9b5de6213ac7c46a3e1a212e8a08cefbbe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 11:50:40 +0200 Subject: [PATCH 0791/1172] {tools}[intel/2015a] networkx 1.10 w/ Python 2.7.10 --- ...networkx-1.10-intel-2015a-Python-2.7.10.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..648339c9c8 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'tools' -- GitLab From 06f86025bdccbd944a7dbd96803abd2e3d5995df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Aug 2015 11:24:33 +0100 Subject: [PATCH 0792/1172] New version of MuTect to use Java 1.7.0_80 --- .../m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-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 new file mode 100644 index 0000000000..1434f1c176 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.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 = 'Tarball' + +name = 'MuTect' +version = '1.1.4' + +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': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 234d3c2efccb7604902eb2ebb88e6bd910520b4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 13:06:00 +0200 Subject: [PATCH 0793/1172] fix remark --- .../p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb index a09ace02c0..b8c14278d8 100644 --- a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb @@ -16,6 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pyver)] +dependencies = [ + (python, pyver), +] moduleclass = 'tools' -- GitLab From c1fe11844f214baee851de286bec8bf765650f0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 13:44:41 +0200 Subject: [PATCH 0794/1172] use GLib 2.44.1 (stable) rather than 2.45.x (development) --- ...{GLib-2.45.2-goolf-1.7.20.eb => GLib-2.44.1-goolf-1.7.20.eb} | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GLib/{GLib-2.45.2-goolf-1.7.20.eb => GLib-2.44.1-goolf-1.7.20.eb} (96%) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb similarity index 96% rename from easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb rename to easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb index 34fcc7fc85..c6424b3f53 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.45.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-goolf-1.7.20.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GLib' -version = '2.45.2' +version = '2.44.1' homepage = 'http://www.gtk.org/' description = """GLib is one of the base libraries of the GTK+ project""" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index d473187b62..41de713278 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.17'), ('freetype', '2.6'), ('fontconfig', '2.11.94'), - ('GLib', '2.45.2'), + ('GLib', '2.44.1'), ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work ('expat', '2.1.0'), ('cairo', '1.14.2'), -- GitLab From ac5f87e94e29c720efab0a0204f7e2506dc45ded Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 14 Aug 2015 13:48:06 +0200 Subject: [PATCH 0795/1172] change GLib version to 2.44.1 --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb index d473187b62..41de713278 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.17'), ('freetype', '2.6'), ('fontconfig', '2.11.94'), - ('GLib', '2.45.2'), + ('GLib', '2.44.1'), ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work ('expat', '2.1.0'), ('cairo', '1.14.2'), -- GitLab From c07bdff4d8552b1960ba44e00e6175365187bd25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 13:59:30 +0200 Subject: [PATCH 0796/1172] {tools,vis}[intel/2015a] Ghostscript 9.16 + cairo 1.14.2 + GLib 2.44.1 --- .../c/cairo/cairo-1.14.2-intel-2015a.eb | 29 +++++++++++++++++ .../g/GLib/GLib-2.44.1-intel-2015a.eb | 21 ++++++++++++ .../Ghostscript-9.16-intel-2015a.eb | 32 +++++++++++++++++++ .../libjpeg-turbo-1.3.1-intel-2015a.eb | 24 ++++++++++++++ .../n/NASM/NASM-2.11.05-intel-2015a.eb | 31 ++++++++++++++++++ 5 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb new file mode 100644 index 0000000000..357e47a331 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.2' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('pixman', '0.32.6'), + ('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/g/GLib/GLib-2.44.1-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb new file mode 100644 index 0000000000..ea740d47ca --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.44.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb new file mode 100644 index 0000000000..1b28614578 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.16' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['829319325bbdb83f5c81379a8f86f38f'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('fontconfig', '2.11.94'), + ('GLib', '2.44.1'), + ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work + ('expat', '2.1.0'), + ('cairo', '1.14.2'), + ('LibTIFF', '4.0.4'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb new file mode 100644 index 0000000000..d6bc643d57 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb new file mode 100644 index 0000000000..9bf8366459 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.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 = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 998adf96b98b156df2f683c724b3bbbab011bb01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 14:15:42 +0200 Subject: [PATCH 0797/1172] add missing fontconfig easyconfig --- .../fontconfig-2.11.94-intel-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.eb new file mode 100644 index 0000000000..df68da2489 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.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': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From c0b14b2bcf357b1da4bcd4e56e4e0a1d464a04b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 14:31:40 +0200 Subject: [PATCH 0798/1172] rename GraphViz dir to fix an issue with case-sensitivity of paths --- .../Graphviz-2.38.0-intel-2014b.eb | 0 ...aphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 68 +++++++++++++++++++ .../Graphviz-2.38.0_icc_sfio.patch | 0 .../Graphviz-2.38.0_icc_vmalloc.patch | 0 4 files changed, 68 insertions(+) rename easybuild/easyconfigs/g/{Graphviz => Graphviz__}/Graphviz-2.38.0-intel-2014b.eb (100%) create mode 100644 easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb rename easybuild/easyconfigs/g/{Graphviz => Graphviz__}/Graphviz-2.38.0_icc_sfio.patch (100%) rename easybuild/easyconfigs/g/{Graphviz => Graphviz__}/Graphviz-2.38.0_icc_vmalloc.patch (100%) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb rename to easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..bc56040508 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.38.0' + +homepage = 'http://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.graphviz.org/pub/graphviz/stable/SOURCES/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + ('cairo', '1.14.2'), + ('expat', '2.1.0'), + ('freetype', '2.6'), + ('fontconfig', '2.11.1'), + ('Ghostscript', '9.16'), + ('GLib', '2.44.1'), + ('GTS', '0.7.6'), + ('Java', '1.7.0_80', '', True), + ('libpng', '1.6.17'), # same version as in freetype + ('Pango', '1.37.2'), + ('Perl', '5.20.0'), + (python, pyver), + ('Qt', '4.8.6', '-GLib-2.44.1'), + ('SWIG', '3.0.7', versionsuffix), + ('Tcl', '8.6.4'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('M4', '1.4.17'), +] + +patches = [ + 'Graphviz-2.38.0_icc_vmalloc.patch', + 'Graphviz-2.38.0_icc_sfio.patch', +] + +configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no ' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +sanity_check_paths = { + 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', + 'lib/libcdt.so', 'lib/libgvc.so', 'lib/libxdot.so'], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/graphviz/python', + 'CLASSPATH': 'lib/graphviz/java/org/graphviz', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_sfio.patch b/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_sfio.patch similarity index 100% rename from easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_sfio.patch rename to easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_sfio.patch diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_vmalloc.patch b/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_vmalloc.patch similarity index 100% rename from easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_vmalloc.patch rename to easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_vmalloc.patch -- GitLab From 51953b8312935755189403ed527ed0889e80c629 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 14:31:59 +0200 Subject: [PATCH 0799/1172] add easyconfig for Qt 4.8.6 on top of GLib 2.44.1 --- .../q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb new file mode 100644 index 0000000000..ba0734aff4 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2015a'} + +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_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] + +glib = 'GLib' +glibver = '2.44.1' +versionsuffix = '-%s-%s' % (glib, glibver) + +dependencies = [ + (glib, glibver), +] + +moduleclass = 'devel' -- GitLab From 232ae2e3d4eb7032fe09adcbf40016507e67807f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 14:32:33 +0200 Subject: [PATCH 0800/1172] rename GraphViz dir back to what it should be --- .../g/{Graphviz__ => Graphviz}/Graphviz-2.38.0-intel-2014b.eb | 0 .../Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 0 .../g/{Graphviz__ => Graphviz}/Graphviz-2.38.0_icc_sfio.patch | 0 .../g/{Graphviz__ => Graphviz}/Graphviz-2.38.0_icc_vmalloc.patch | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{Graphviz__ => Graphviz}/Graphviz-2.38.0-intel-2014b.eb (100%) rename easybuild/easyconfigs/g/{Graphviz__ => Graphviz}/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb (100%) rename easybuild/easyconfigs/g/{Graphviz__ => Graphviz}/Graphviz-2.38.0_icc_sfio.patch (100%) rename easybuild/easyconfigs/g/{Graphviz__ => Graphviz}/Graphviz-2.38.0_icc_vmalloc.patch (100%) diff --git a/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2014b.eb rename to easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb rename to easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_sfio.patch b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_sfio.patch similarity index 100% rename from easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_sfio.patch rename to easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_sfio.patch diff --git a/easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_vmalloc.patch b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_vmalloc.patch similarity index 100% rename from easybuild/easyconfigs/g/Graphviz__/Graphviz-2.38.0_icc_vmalloc.patch rename to easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0_icc_vmalloc.patch -- GitLab From c5ac4f74d52223a9d13dcbbe6180f8f664850a48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 14:41:24 +0200 Subject: [PATCH 0801/1172] add missing stuffz --- ...Object-Introspection-1.45.3-intel-2015a.eb | 35 + .../g/GTS/GTS-0.7.6-intel-2015a.eb | 25 + .../h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb | 33 + .../p/PCRE/PCRE-8.37-intel-2015a.eb | 18 + .../p/Pango/Pango-1.37.2-intel-2015a.eb | 43 + .../p/Perl/Perl-5.20.0-intel-2015a.eb | 870 ++++++++++++++++++ ...aphviz-1.3rc2-intel-2015a-Python-2.7.10.eb | 24 + .../SWIG-3.0.7-intel-2015a-Python-2.7.10.eb | 23 + 8 files changed, 1071 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb new file mode 100644 index 0000000000..f2480702d7 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.45.3' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.10'), + ('GLib', '2.40.0'), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), +] + +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']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb new file mode 100644 index 0000000000..805dcbaf50 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.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': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.40.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.so', 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb new file mode 100644 index 0000000000..525aebfda0 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.0.1' + +homepage = 'http://www.harfbuzz.org/' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('cairo', '1.14.2'), + ('GObject-Introspection', '1.45.3'), +] + +patches = ['HarfBuzz-%(version)s_config.patch'] + +configopts = '--with-gobject --enable-introspection=yes ' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.so', 'bin/hb-view'], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb new file mode 100644 index 0000000000..1218fbc5d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.37' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb new file mode 100644 index 0000000000..23a55680b8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.37.2' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/pango/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('cairo', '1.14.2'), + ('fontconfig', '2.11.1'), + ('freetype', '2.6'), + ('GLib', '2.40.0'), + ('HarfBuzz', '1.0.1'), + ('GObject-Introspection', '1.45.3'), + ('libXft', '2.3.2', '-libX11-1.6.3'), +] + +builddependencies = [ + ('M4', '1.4.17'), +] + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.so', 'lib/libpangocairo-1.0.so', + 'lib/libpangoft2-1.0.so', 'lib/libpangoxft-1.0.so'], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb new file mode 100644 index 0000000000..6577079508 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb @@ -0,0 +1,870 @@ +name = 'Perl' +version = '5.20.0' + +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 = [ + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('DBI', '1.631', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], + }), + ('Module::Build', '0.4205', { + 'source_tmpl': 'Module-Build-0.4205.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Devel::StackTrace', '1.32', { + 'source_tmpl': 'Devel-StackTrace-1.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('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/'], + }), + ('Exception::Class', '1.38', { + 'source_tmpl': 'Exception-Class-1.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Tester', '0.109', { + 'source_tmpl': 'Test-Tester-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FD/FDALY/'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Deep', '0.112', { + 'source_tmpl': 'Test-Deep-0.112.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Algorithm::Diff', '1.15', { + 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], + }), + ('Text::Diff', '1.41', { + 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Differences', '0.61', { + 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Sub::Uplevel', '0.24', { + 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Exception', '0.32', { + 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Test::Most', '0.33', { + 'source_tmpl': 'Test-Most-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('File::Slurp::Tiny', '0.003', { + 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Tree::DAG_Node', '1.22', { + 'source_tmpl': 'Tree-DAG_Node-1.22.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Try::Tiny', '0.20', { + 'source_tmpl': 'Try-Tiny-0.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Test::Fatal', '0.013', { + 'source_tmpl': 'Test-Fatal-0.013.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Test::Requires', '0.07', { + 'source_tmpl': 'Test-Requires-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM/'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', '0.927', { + 'source_tmpl': 'Sub-Install-0.927.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Capture::Tiny', '0.24', { + 'source_tmpl': 'Capture-Tiny-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', '0.07', { + 'source_tmpl': 'Module-Implementation-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('List::MoreUtils', '0.33', { + 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Package::DeprecationManager', '0.13', { + 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', '0.36', { + 'source_tmpl': 'Package-Stash-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('TAP::Harness::Env', '3.30', { + 'source_tmpl': 'Test-Harness-3.30.tar.gz', + 'source_urls': ['http://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'], + }), + ('ExtUtils::Config', '0.007', { + 'source_tmpl': 'ExtUtils-Config-0.007.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::InstallPaths', '0.010', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.010.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.036', { + 'source_tmpl': 'Module-Build-Tiny-0.036.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Class::Load', '0.21', { + 'source_tmpl': 'Class-Load-0.21.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], + }), + ('Eval::Closure', '0.11', { + 'source_tmpl': 'Eval-Closure-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('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/'], + }), + ('Devel::GlobalDestruction', '0.12', { + 'source_tmpl': 'Devel-GlobalDestruction-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('boolean', '0.32', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('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/'], + }), + ('Class::Load::XS', '0.08', { + 'source_tmpl': 'Class-Load-XS-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Moose', '2.1208', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Params::Validate', '1.10', { + 'source_tmpl': 'Params-Validate-1.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime::Locale', '0.45', { + 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('DateTime::TimeZone', '1.70', { + 'source_tmpl': 'DateTime-TimeZone-1.70.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Warnings', '0.014', { + 'source_tmpl': 'Test-Warnings-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('DateTime', '1.10', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', '1.00', { + 'source_tmpl': 'IO-HTML-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('URI', '1.60', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Encode::Locale', '1.03', { + 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['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece', '1.27', { + 'source_tmpl': 'Time-Piece-1.27.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('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/'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('version', '0.9908', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('XML::SAX::Writer', '0.54', { + 'source_tmpl': 'XML-SAX-Writer-0.54.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT/'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('DBD::SQLite', '1.42', { + 'source_tmpl': 'DBD-SQLite-1.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN/'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD/'], + }), + ('Params::Validate', '1.13', { + 'source_tmpl': 'Params-Validate-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Term::ReadKey', '2.32', { + 'source_tmpl': 'TermReadKey-2.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JS/JSTOWE/'], + 'patches': ['TermReadKey-2.32.patch'], + }), + ('Moo', '1.005000', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('strictures', '1.005004', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('File::Find::Rule::Perl', '1.13', { + 'source_tmpl': 'File-Find-Rule-Perl-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Version', '1.002004', { + 'source_tmpl': 'Test-Version-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/X/XE/XENO/'], + }), + ('Test::Harness', '3.32', { + 'source_tmpl': 'Test-Harness-3.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Import::Into', '1.002004', { + 'source_tmpl': 'Import-Into-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('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/'], + }), + ('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/'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('IPC::Run3', '0.03', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Want', '0.23', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/'], + }), + ('Log::Handler', '0.82', { + 'source_tmpl': 'Log-Handler-0.82.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BL/BLOONIX/'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('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/'], + }), + ('DBIx::Admin::TableInfo', '2.11', { + 'source_tmpl': 'DBIx-Admin-TableInfo-2.11.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Carp', '1.3301', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Exporter', '5.70', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Scalar::Util', '1.39', { + 'source_tmpl': 'Scalar-List-Utils-1.39.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PEVANS/'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM/'], + }), + ('HTTP::Tiny', '0.043', { + 'source_tmpl': 'HTTP-Tiny-0.043.tar.gz', + 'source_urls': ['http://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'], + }), + ('Text::Balanced', '2.02', { + 'source_tmpl': 'Text-Balanced-2.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Parse::RecDescent', '1.967009', { + 'source_tmpl': 'Parse-RecDescent-1.967009.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JT/JTBRAUN/'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL/'], + }), + ('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/'], + }), + ('Lingua::EN::PluralToSingular', '0.13', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB/'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..ba6e1cf97c --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pygraphviz' +version = '1.3rc2' + +homepage = 'https://pypi.python.org/pypi/pycosat' +description = """pycosat provides efficient Python bindings to picosat on the C level, i.e. when importing pycosat, + the picosat solver becomes part of the Python process itself.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('Graphviz', '2.38.0', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..95fbf9613d --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.7' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.37'), +] + +moduleclass = 'devel' -- GitLab From 8ae177c52a03aad027c3afb6738753fef9a9d8d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 16:01:42 +0200 Subject: [PATCH 0802/1172] use lowopt in Ghostscript easyconfig to dance around internal compiler error being triggered --- .../easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb index 1b28614578..691a90006b 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb @@ -8,7 +8,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t different targets. It used to be part of the cups printing stack, but is no longer used for that.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'pic': True} +# lowopt (-O1) is used to avoid internal compiler error that is hit when -O2 is used +toolchainopts = {'pic': True, 'lowopt': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 973d4fecdf4f220bb0074e089d2c60cf0b904e04 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 14 Aug 2015 16:08:20 +0200 Subject: [PATCH 0803/1172] iThis wil be undone --- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 ++- .../i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb | 3 ++- .../easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 ++- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb | 3 ++- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 ++- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 ++- .../easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 ++- .../i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 ++- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 ++- .../i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 ++- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 ++- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb | 3 ++- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 ++- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 ++- .../easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 ++- .../i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 ++- .../i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 ++- .../impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 ++- .../easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 ++- .../easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 ++- 34 files changed, 68 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 5f35cd6834..67fe1c9fd2 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 437532bb49..40250b2b6b 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -19,4 +19,5 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb index b47595dda3..319b5beee6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb @@ -18,4 +18,5 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb index 7b8162cea3..7bd42b8b54 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index a551f57786..50fbae5fd2 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb index 153ba081b1..86e1c0a192 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb @@ -18,4 +18,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb index da8581e61f..e4c11fe75f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb @@ -18,4 +18,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 4830b5c3c8..8a621e4fe8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -18,4 +18,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb index 16a82416aa..ba91117d77 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb index d81cc168ff..6cac21b8ef 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 839fe8f604..3746b5d71a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 0f49c7d212..628120ec39 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 178d95d415..537c39aa33 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 16d697d706..0143f60407 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 875b582066..3d7c2323e0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 00ee030d34..79a7e9efb0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 1440a8a1b0..e2c51dad97 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb index f3bb7b6e5e..a7fdb6dc05 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 97c88ff999..399200902f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 839d937043..7cc827a94b 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 1b64e97c46..42cd5fe8c9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index d31c2924c8..2a683761dc 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 478cc2645d..655d33f7c0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index ddba0fe1d6..05c4ee41f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5732c5fbd3..1f82b191f3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb index b9d7d5e20b..d4ee84fdf1 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index e55725a62a..a4d642e164 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 5f63a18d7b..d7c5e033be 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 43da00f4ab..d6df12b6ca 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 64a9011ae4..5ed216f126 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index d23a27639e..be351ecc9f 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 0cc5dc235f..8904676b97 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index 5e0972d8f3..6c35863a75 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -16,4 +16,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index fb7853e6f5..1c0482c92f 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -17,4 +17,5 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -moduleclass = 'mpi' +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) + = 'mpi' -- GitLab From 2241e5f7a9e7353861168cc198ac2639422e393d Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 14 Aug 2015 16:08:39 +0200 Subject: [PATCH 0804/1172] Revert "iThis wil be undone" This reverts commit 973d4fecdf4f220bb0074e089d2c60cf0b904e04. --- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 +-- .../i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb | 3 +-- .../easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 +-- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb | 3 +-- .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 +-- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 +-- .../i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 +-- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 +-- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 +-- .../i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 +-- .../i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 +-- .../impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 +-- .../easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 +-- 34 files changed, 34 insertions(+), 68 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 67fe1c9fd2..5f35cd6834 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 40250b2b6b..437532bb49 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -19,5 +19,4 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb index 319b5beee6..b47595dda3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb @@ -18,5 +18,4 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb index 7bd42b8b54..7b8162cea3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index 50fbae5fd2..a551f57786 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb index 86e1c0a192..153ba081b1 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb @@ -18,5 +18,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb index e4c11fe75f..da8581e61f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb @@ -18,5 +18,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 8a621e4fe8..4830b5c3c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -18,5 +18,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb index ba91117d77..16a82416aa 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb index 6cac21b8ef..d81cc168ff 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 3746b5d71a..839fe8f604 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 628120ec39..0f49c7d212 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 537c39aa33..178d95d415 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 0143f60407..16d697d706 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 3d7c2323e0..875b582066 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 79a7e9efb0..00ee030d34 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index e2c51dad97..1440a8a1b0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb index a7fdb6dc05..f3bb7b6e5e 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 399200902f..97c88ff999 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 7cc827a94b..839d937043 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 42cd5fe8c9..1b64e97c46 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index 2a683761dc..d31c2924c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 655d33f7c0..478cc2645d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 05c4ee41f8..ddba0fe1d6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 1f82b191f3..5732c5fbd3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb index d4ee84fdf1..b9d7d5e20b 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index a4d642e164..e55725a62a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index d7c5e033be..5f63a18d7b 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index d6df12b6ca..43da00f4ab 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 5ed216f126..64a9011ae4 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index be351ecc9f..d23a27639e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 8904676b97..0cc5dc235f 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index 6c35863a75..5e0972d8f3 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -16,5 +16,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 1c0482c92f..fb7853e6f5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -17,5 +17,4 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) - = 'mpi' +moduleclass = 'mpi' -- GitLab From 0c8d893bb895f8ce9c636548fe1a49bbccb50183 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 14 Aug 2015 16:09:29 +0200 Subject: [PATCH 0805/1172] Add comment on mpi wrappers to all impi eb files --- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 +++ .../i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb | 3 +++ .../easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 +++ .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb | 3 +++ .../easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 +++ .../i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +++ .../easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 +++ .../i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 +++ .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 +++ .../i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +++ .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 +++ .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb | 3 +++ easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 +++ .../i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 +++ .../easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 +++ .../i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 +++ .../i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 +++ .../impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +++ .../easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 +++ .../easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 +++ 34 files changed, 102 insertions(+) diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 5f35cd6834..e0aa55d8e1 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 437532bb49..ed9f544efd 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -19,4 +19,7 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb index b47595dda3..cdfb37e60d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb @@ -18,4 +18,7 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb index 7b8162cea3..05a3dcd524 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index a551f57786..6a5c58b965 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb index 153ba081b1..32c938b850 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb index da8581e61f..c9a73b1fbd 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 4830b5c3c8..321fcf953c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb index 16a82416aa..03f1826816 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb index d81cc168ff..61d1d12258 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 839fe8f604..52c5610522 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 0f49c7d212..10206cc86f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 178d95d415..14cfad4a95 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 16d697d706..5e54731d6a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 875b582066..9d7dcdffc5 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 00ee030d34..5b383c2276 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 1440a8a1b0..2aeefc2cd9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb index f3bb7b6e5e..6f91af21b3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 97c88ff999..48ea7b9ce5 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 839d937043..d88a37c91f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 1b64e97c46..048251c331 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index d31c2924c8..5843dfe200 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 478cc2645d..9e56e74b2d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index ddba0fe1d6..07bd2d77cd 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5732c5fbd3..d3e34f99af 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb index b9d7d5e20b..54e5d17b0f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index e55725a62a..23f4c48744 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 5f63a18d7b..57ed02ab9a 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 43da00f4ab..107a4290a3 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 64a9011ae4..85451943cd 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index d23a27639e..0bd01e5fe2 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 0cc5dc235f..7b891134eb 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index 5e0972d8f3..baf8e132f9 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index fb7853e6f5..10fe208f63 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -17,4 +17,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' -- GitLab From d368eff27f765b540a9d348441a67ed79ed39ee1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 16:14:53 +0200 Subject: [PATCH 0806/1172] drop patch for HarfBuzz 1.0.1 --- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb index 525aebfda0..459de39ca5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -16,8 +16,6 @@ dependencies = [ ('GObject-Introspection', '1.45.3'), ] -patches = ['HarfBuzz-%(version)s_config.patch'] - configopts = '--with-gobject --enable-introspection=yes ' sanity_check_paths = { -- GitLab From c85fdf4523153c6535c237b8e8eb53a941d600ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 17:05:45 +0200 Subject: [PATCH 0807/1172] fix version of GObject-Introspection, must match major.minor of GLib --- ...l-2015a.eb => GObject-Introspection-1.44.0-intel-2015a.eb} | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GObject-Introspection/{GObject-Introspection-1.45.3-intel-2015a.eb => GObject-Introspection-1.44.0-intel-2015a.eb} (96%) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb similarity index 96% rename from easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb rename to easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb index f2480702d7..a78661727e 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.45.3-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.44.0-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GObject-Introspection' -version = '1.45.3' +version = '1.44.0' homepage = 'https://wiki.gnome.org/GObjectIntrospection/' description = """GObject introspection is a middleware layer between C libraries @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('Python', '2.7.10'), - ('GLib', '2.40.0'), + ('GLib', '2.44.1'), ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb index 459de39ca5..dc943975f0 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_BZ2] dependencies = [ ('cairo', '1.14.2'), - ('GObject-Introspection', '1.45.3'), + ('GObject-Introspection', '1.44.1'), ] configopts = '--with-gobject --enable-introspection=yes ' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb index 23a55680b8..25ff2efb9f 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6'), ('GLib', '2.40.0'), ('HarfBuzz', '1.0.1'), - ('GObject-Introspection', '1.45.3'), + ('GObject-Introspection', '1.44.1'), ('libXft', '2.3.2', '-libX11-1.6.3'), ] -- GitLab From 7ac39b36db1b4d3cef1db291f6fa3daa1e706756 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 17:09:02 +0200 Subject: [PATCH 0808/1172] fix typo --- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb index dc943975f0..d96b54ef93 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_BZ2] dependencies = [ ('cairo', '1.14.2'), - ('GObject-Introspection', '1.44.1'), + ('GObject-Introspection', '1.44.0'), ] configopts = '--with-gobject --enable-introspection=yes ' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb index 25ff2efb9f..866d5d26db 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6'), ('GLib', '2.40.0'), ('HarfBuzz', '1.0.1'), - ('GObject-Introspection', '1.44.1'), + ('GObject-Introspection', '1.44.0'), ('libXft', '2.3.2', '-libX11-1.6.3'), ] -- GitLab From 6e0a76a71569c1446b9946ceb14fd0fb0bc9b71c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 17:35:01 +0200 Subject: [PATCH 0809/1172] fix remarks --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb | 3 ++- easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb | 2 +- .../easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb | 1 + .../easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb | 2 +- ...uzz_no_symbolic.patch => HarfBuzz-0.9.41_no_symbolic.patch} | 0 .../easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb | 1 - easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb | 1 + 7 files changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HarfBuzz/{HarfBuzz_no_symbolic.patch => HarfBuzz-0.9.41_no_symbolic.patch} (100%) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb index f484250400..30174bd67f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2015a.eb @@ -4,7 +4,8 @@ easyblock = 'ConfigureMake' homepage = 'http://www.gtk.org/' description = """GLib is one of the base libraries of the GTK+ project""" -toolchain = {'name': 'intel', 'version': '2015a'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) + +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb index 9102a3d424..64f2f5e526 100644 --- a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.41.2-intel-2015a.eb @@ -13,7 +13,7 @@ source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_mi sources = ['%(namelower)s-%(version)s.tar.xz'] dependencies = [ - ('GLib', '%(version)s'), + ('GLib', version), ('libsigc++', '2.4.1'), ] diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb index 3d4350cb57..bb9b01af4f 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'gdk-pixbuf' version = '2.31.4' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb index 407a30edff..30ed702ef8 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['HarfBuzz_no_symbolic.patch'] +patches = ['HarfBuzz-%(version)s_no_symbolic.patch'] dependencies = [ ('cairo', '1.14.2'), diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41_no_symbolic.patch similarity index 100% rename from easybuild/easyconfigs/h/HarfBuzz/HarfBuzz_no_symbolic.patch rename to easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41_no_symbolic.patch diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb index 966ef00954..f4b4e3a392 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb @@ -18,4 +18,3 @@ sanity_check_paths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb index 78e015464a..6797ad144b 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb @@ -1,4 +1,5 @@ easyblock = 'ConfigureMake' + name = 'Pango' version = '1.37.1' -- GitLab From 37170e101f6b206cd55fc2d71282ceb511892c8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 17:55:00 +0200 Subject: [PATCH 0810/1172] {phys}[intel/2015a] FDS r18915 --- .../f/FDS/FDS-r18915-intel-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb new file mode 100644 index 0000000000..3826bdc124 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' -- GitLab From 3a1d82a0ff7c1e96300865fda7fd56228c3a2e91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 18:09:20 +0200 Subject: [PATCH 0811/1172] make texinfo a build dep in bc easyconfig --- easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb index d9c14913b3..1d80e71dae 100644 --- a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb @@ -20,6 +20,8 @@ dependencies = [ ('libreadline','6.3'), ('flex','2.5.38'), ('Bison','3.0.2'), +] +builddependencies = [ ('texinfo','5.2'), ] -- GitLab From 3ed9328e32077f32f0163f02e959a219b3ca7467 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 20:47:30 +0200 Subject: [PATCH 0812/1172] use FTPGNOME_SOURCE --- .../GObject-Introspection-1.44.0-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 a78661727e..0461a34f5f 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 @@ -12,7 +12,7 @@ description = """GObject introspection is a middleware layer between C libraries toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb index 866d5d26db..c45f2be616 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -12,7 +12,7 @@ description = """Pango is a library for laying out and rendering of text, with a toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/pango/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ -- GitLab From 305d37b147dd2730fa3793a8db1ff313c5640531 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Aug 2015 20:49:40 +0200 Subject: [PATCH 0813/1172] use FTPGNOME_SOURCE where applicable --- .../GObject-Introspection-1.42.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb | 2 +- 2 files changed, 2 insertions(+), 2 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 73dfcfd2e8..7ae4e4f769 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 @@ -12,7 +12,7 @@ description = """GObject introspection is a middleware layer between C libraries toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index 1de69091f3..76a476c789 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -12,7 +12,7 @@ description = """Pango is a library for laying out and rendering of text, with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/pango/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ -- GitLab From 264fe8f49a5ad6606a2e8f1f86083f7141e4bf8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 00:03:39 +0200 Subject: [PATCH 0814/1172] {math}[intel/2015a] MUMPS 5.0.1 w/ METIS/ParMETIS --- .../m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb | 22 +++++++++++++++++++ .../MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb new file mode 100644 index 0000000000..a7272f2a49 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb @@ -0,0 +1,22 @@ +name = 'MUMPS' +version = '5.0.1' +versionsuffix = '-metis' + +homepage = 'http://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('SCOTCH', '6.0.4'), + ('METIS', '5.1.0'), +] + +parallel = 1 +buildopts = 'all' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb new file mode 100644 index 0000000000..d258742e32 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb @@ -0,0 +1,22 @@ +name = 'MUMPS' +version = '5.0.1' +versionsuffix = '-parmetis' + +homepage = 'http://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('SCOTCH', '6.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 +buildopts = 'all' + +moduleclass = 'math' -- GitLab From 3dd9dc5cb02b0bf1a36b69d18438c7bb82ce653c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 01:25:48 +0200 Subject: [PATCH 0815/1172] {lib}[intel/2015a] Global Arrays 5.3 --- .../GlobalArrays-5.3-intel-2015a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb new file mode 100644 index 0000000000..160dbeb127 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.3' +versionsuffix = '-openib' + +homepage = 'http://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://hpc.pnl.gov/globalarrays/download/'] +sources = ['ga-%(version_major)s-%(version_minor)s.tgz'] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +configopts = '--with-openib' +configopts += ' --with-blas8="-L$BLAS_LIB_DIR $LIBBLAS" --with-lapack="-L$LAPACK_LIB_DIR $LIBLAPACK"' +configopts += ' --with-scalapack8="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK"' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' -- GitLab From 49cce175ea0467da2b3c1c50cc3058bdea28dc5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 01:41:27 +0200 Subject: [PATCH 0816/1172] fix easyconfig filename for Global Arrays easyconfig --- ...-5.3-intel-2015a.eb => GlobalArrays-5.3-intel-2015a-openib.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GlobalArrays/{GlobalArrays-5.3-intel-2015a.eb => GlobalArrays-5.3-intel-2015a-openib.eb} (100%) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb similarity index 100% rename from easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a.eb rename to easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb -- GitLab From 26605fdab073ad052322c0657734fab0f50041c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 10:07:43 +0200 Subject: [PATCH 0817/1172] fix source_urls and minor style issues --- .../m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb index 14ede40f79..c0d5b7bd44 100644 --- a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'MACS' version = '1.4.2-1' @@ -18,7 +18,7 @@ description = """ Model-based Analysis of ChIP-Seq (MACS) on short reads sequenc toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://github.com/downloads/taoliu/MACS/'] +source_urls = ['https://cloud.github.com/downloads/taoliu/MACS/'] sources = [SOURCE_TAR_GZ] python = 'Python' @@ -27,12 +27,12 @@ pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) -options = {'modulename': 'MACS14'} - dependencies = [ (python, pyver), ] +options = {'modulename': 'MACS14'} + sanity_check_paths = { 'files': ['bin/macs14'], 'dirs': [''], -- GitLab From 01321bcaf4c8220a42bd77a3d8160a892a4d20ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 10:18:37 +0200 Subject: [PATCH 0818/1172] transform broken source URLs into a comment --- .../m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb index c0d5b7bd44..fe54887474 100644 --- a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -18,7 +18,7 @@ description = """ Model-based Analysis of ChIP-Seq (MACS) on short reads sequenc toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://cloud.github.com/downloads/taoliu/MACS/'] +# automagic download doesn't work, download manually from https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From a61b6d91b4c624933ec0bef88b262f22104db10b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 11:02:12 +0200 Subject: [PATCH 0819/1172] fix conflict detection in unit 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 b8219c692d..fa238d1cb0 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -149,7 +149,7 @@ class EasyConfigTest(TestCase): depmap = {} for spec in self.ordered_specs: build_deps = map(mk_dep_mod_name, spec['builddependencies']) - deps = map(mk_dep_mod_name, spec['dependencies']) + deps = map(mk_dep_mod_name, spec['ec'].all_dependencies) # 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)) -- GitLab From ec17b3b52ee1fc69dc955b1d3a059d4093dc8d5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 18:54:05 +0200 Subject: [PATCH 0820/1172] exclude external modules from conflicts check, make sure EasyBuildMNS is used --- test/easyconfigs/easyconfigs.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index fa238d1cb0..a766a187d2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -44,13 +44,14 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig +from easybuild.framework.easyconfig.easyconfig import EasyConfig 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.filetools import write_file 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 @@ -143,13 +144,15 @@ class EasyConfigTest(TestCase): self.process_all_easyconfigs() def mk_dep_mod_name(spec): - return tuple(ActiveMNS().det_full_module_name(spec).split(os.path.sep)) + 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: - build_deps = map(mk_dep_mod_name, spec['builddependencies']) - deps = map(mk_dep_mod_name, spec['ec'].all_dependencies) + # 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['external_module']] + deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d['external_module']] + # 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)) -- GitLab From dacd44fc5b95b6074388aa08b591d84e68f28271 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 21:13:31 +0200 Subject: [PATCH 0821/1172] align dep version in Pango easyconfig --- .../libX11-1.6.3-intel-2015a-Python-2.7.10.eb | 37 +++++++++++++++++++ ...-intel-2015a-libX11-1.6.3-Python-2.7.10.eb | 34 +++++++++++++++++ .../p/Pango/Pango-1.37.2-intel-2015a.eb | 6 +-- 3 files changed, 74 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..9c513d4634 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +dependencies = [ + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), +] + +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/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb new file mode 100644 index 0000000000..a7d92d4af4 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.10'), + ('libXrender', '0.9.9'), + ('freetype', '2.6'), + ('fontconfig', '2.11.94'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb index c45f2be616..d1b5731cff 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -17,12 +17,12 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('cairo', '1.14.2'), - ('fontconfig', '2.11.1'), + ('fontconfig', '2.11.94'), ('freetype', '2.6'), - ('GLib', '2.40.0'), + ('GLib', '2.44.1'), ('HarfBuzz', '1.0.1'), ('GObject-Introspection', '1.44.0'), - ('libXft', '2.3.2', '-libX11-1.6.3'), + ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), ] builddependencies = [ -- GitLab From c27e6c665dbaf50c3d1432968f6f8db69cbb9a29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 21:15:13 +0200 Subject: [PATCH 0822/1172] fix versionsuffix in libXft easyconfig --- .../libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb index a7d92d4af4..9298667cf5 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb @@ -17,10 +17,11 @@ builddependencies = [ ] libx11ver = '1.6.3' -versionsuffix = '-libX11-%s' % libx11ver +pysuff = '-Python-2.7.10' +versionsuffix = '-libX11-%s%s' % (libx11ver, pysuff) dependencies = [ - ('libX11', libx11ver, '-Python-2.7.10'), + ('libX11', libx11ver, pysuff), ('libXrender', '0.9.9'), ('freetype', '2.6'), ('fontconfig', '2.11.94'), -- GitLab From 14104d7ac59d70a0bb4f9dbc14abbf4eb775adf7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 21:22:29 +0200 Subject: [PATCH 0823/1172] include missing easyconfigs --- .../libxcb-1.11-intel-2015a-Python-2.7.10.eb | 34 +++++++++++++++++++ ...cb-proto-1.11-intel-2015a-Python-2.7.10.eb | 27 +++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..c1b10ef129 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('xcb-proto', '1.11', versionsuffix), + ('libXau', '1.0.8'), + ('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' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..32ea56a932 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' -- GitLab From fbb42f76d6becbe59757a0fdb7066271295f76ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 21:44:06 +0200 Subject: [PATCH 0824/1172] fix dep conflict on libX11 --- ...-intel-2015a-libX11-1.6.3-Python-2.7.10.eb | 2 +- ...Xrender-0.9.9-intel-2015a-Python-2.7.10.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb index 9298667cf5..306d472838 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb @@ -22,7 +22,7 @@ versionsuffix = '-libX11-%s%s' % (libx11ver, pysuff) dependencies = [ ('libX11', libx11ver, pysuff), - ('libXrender', '0.9.9'), + ('libXrender', '0.9.9', pysuff), ('freetype', '2.6'), ('fontconfig', '2.11.94'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..e6f3cd47ac --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From e09059e65af86c30fa77a97a78df09204c59d5f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 21:58:34 +0200 Subject: [PATCH 0825/1172] fix more dep conflicts --- ....7.6-intel-2015a.eb => GTS-0.7.6-intel-2015a-GLib-2.44.1.eb} | 2 +- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GTS/{GTS-0.7.6-intel-2015a.eb => GTS-0.7.6-intel-2015a-GLib-2.44.1.eb} (95%) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb similarity index 95% rename from easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb rename to easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb index 805dcbaf50..7a74d42709 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('GLib', '2.40.0'), + ('GLib', '2.44.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index bc56040508..ea3d8182b7 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -23,7 +23,7 @@ dependencies = [ ('cairo', '1.14.2'), ('expat', '2.1.0'), ('freetype', '2.6'), - ('fontconfig', '2.11.1'), + ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), ('GLib', '2.44.1'), ('GTS', '0.7.6'), -- GitLab From 5e5146ccc129477a662c3b14ae42b259c58a895b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 22:14:27 +0200 Subject: [PATCH 0826/1172] fix versionsuffix in GTS easyconfig --- .../easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb index 7a74d42709..8b0fa88d6e 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb @@ -13,8 +13,12 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +glib = 'GLib' +gliver = '2.44.1' +versionsuffix = '-%s'-%s' % (glib, glibver) + dependencies = [ - ('GLib', '2.44.1'), + (glib, glibver), ] sanity_check_paths = { -- GitLab From eacb4f7f9a1dc5bc0e47836e3310e9838b43d1a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 22:26:10 +0200 Subject: [PATCH 0827/1172] fix versionsuffux for GTS in Graphviz easyconfig --- .../Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index ea3d8182b7..c5e6a0512b 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -19,20 +19,21 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) +glibsuff = '-GLib-2.44.1' + dependencies = [ ('cairo', '1.14.2'), ('expat', '2.1.0'), ('freetype', '2.6'), ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), - ('GLib', '2.44.1'), - ('GTS', '0.7.6'), + ('GTS', '0.7.6', glibsuff), ('Java', '1.7.0_80', '', True), - ('libpng', '1.6.17'), # same version as in freetype + ('libpng', '1.6.17'), ('Pango', '1.37.2'), ('Perl', '5.20.0'), (python, pyver), - ('Qt', '4.8.6', '-GLib-2.44.1'), + ('Qt', '4.8.6', glibsuff), ('SWIG', '3.0.7', versionsuffix), ('Tcl', '8.6.4'), ('zlib', '1.2.8'), -- GitLab From 02b7056c9936b0aecd98036cd34c86705270e12b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Aug 2015 22:37:11 +0200 Subject: [PATCH 0828/1172] fix typo --- .../easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb index 8b0fa88d6e..959c6d7b2b 100644 --- a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb @@ -14,8 +14,8 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] glib = 'GLib' -gliver = '2.44.1' -versionsuffix = '-%s'-%s' % (glib, glibver) +glibver = '2.44.1' +versionsuffix = '-%s-%s' % (glib, glibver) dependencies = [ (glib, glibver), -- GitLab From 78e8268989d2435575f75b26a9471656578e04a4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 15 Aug 2015 23:52:35 +0100 Subject: [PATCH 0829/1172] Update Biostrings for intel toolchain --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 51ca069167..ab6e118044 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -48,7 +48,7 @@ exts_list = [ ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.2', bioconductor_options), + ('Biostrings', '2.36.3', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), -- GitLab From ad1d02dc26dc264bdb4a0bdd0049e0e9f597b9b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 09:47:24 +0200 Subject: [PATCH 0830/1172] Revert "Update versions on @boegel's request." This reverts commit 1e3d5ae4324d43c05bca0c8ba595b16a8f8400c8. --- .../easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.10-intel-2015a.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 39e03ec1d8..acee13ba04 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -120,22 +120,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.8', { + ('Jinja2', '2.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.9', { + ('jsonpointer', '1.7', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.5.1', { + ('jsonschema', '2.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-2', { + ('functools32', '3.2.3-1', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.7', { + ('mistune', '0.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.2.1', { + ('tornado', '4.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 3ada190dc7..9534ab01b3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -120,22 +120,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.8', { + ('Jinja2', '2.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.9', { + ('jsonpointer', '1.7', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.5.1', { + ('jsonschema', '2.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-2', { + ('functools32', '3.2.3-1', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.7', { + ('mistune', '0.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.2.1', { + ('tornado', '4.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { -- GitLab From 04d41ea3999954279db9c6e4d56fab08058569bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 09:47:32 +0200 Subject: [PATCH 0831/1172] Revert "Remove change from 2.7.9 and add it to the foss version." This reverts commit e5218465e93a8777b7d9d532b79cf7848ce12e42. --- .../p/Python/Python-2.7.10-foss-2015a.eb | 24 ------------------- .../p/Python/Python-2.7.9-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index acee13ba04..8e4cfabe9d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -117,30 +117,6 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], - }), - ('Jinja2', '2.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('jsonpointer', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 2c04d1e9a7..8b74208902 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,6 +114,30 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' -- GitLab From 5bc5d1032de86c5675e17079067208afb3405510 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 09:47:40 +0200 Subject: [PATCH 0832/1172] Revert "Add libraries for Python which are used for IPython notebook." This reverts commit 18e06c15ee1de5e40b63a5313ca10070b3613750. --- .../p/Python/Python-2.7.10-intel-2015a.eb | 24 ------------------- .../p/Python/Python-2.7.9-intel-2015a.eb | 24 ------------------- 2 files changed, 48 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 9534ab01b3..f5c2309ea8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -117,30 +117,6 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], - }), - ('Jinja2', '2.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('jsonpointer', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 8b74208902..2c04d1e9a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,30 +114,6 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], - }), - ('Jinja2', '2.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('jsonpointer', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' -- GitLab From 6a1ea073bcd74f00dcf4d1016d945edc2addcefe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 09:51:31 +0200 Subject: [PATCH 0833/1172] Revert "sync up easyconfig for Python 2.7.10 with intel/2015b w.r.t. exts_list" This reverts commit 98aba288fd622c4aaf0797ad28e0247d4665163c. --- .../p/Python/Python-2.7.10-intel-2015b.eb | 24 ------------------- 1 file changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 58596bda71..a5115dc2be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -116,30 +116,6 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('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'], - }), - ('jsonpointer', '1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' -- GitLab From 9afda3fb9173ba49979a30c5e7a4d500ea37ba75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 09:52:12 +0200 Subject: [PATCH 0834/1172] Revert "sync up easyconfig for Python 2.7.10 with foss/2015b w.r.t. exts_list" This reverts commit 7489172a48f240698853bb3d977d55c8a681d4b2. --- .../p/Python/Python-2.7.10-foss-2015b.eb | 24 ------------------- 1 file changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 87c42e20b7..8d705315cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -116,30 +116,6 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('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'], - }), - ('jsonpointer', '1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' -- GitLab From 4c953b1a7ee2bd89f3900a5684263f690810f1a4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 17 Aug 2015 10:21:06 +0200 Subject: [PATCH 0835/1172] PSI4 version with maxam=7 --- .../PSI-4.0b6-20150814-fix-gitversion.patch | 12 ++++++ ...SI-4.0b6-20150814-intel-2015a-mt-maxam7.eb | 38 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch new file mode 100644 index 0000000000..7f36d862a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch @@ -0,0 +1,12 @@ +# As we have a git version without the git metadata, we tell it which commit we have used +# by wpoely86@gmail.com +diff -ur psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3.orig/src/bin/psi4/gitversion.py psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3/src/bin/psi4/gitversion.py +--- psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3.orig/src/bin/psi4/gitversion.py 2015-08-14 04:47:54.000000000 +0200 ++++ psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3/src/bin/psi4/gitversion.py 2015-08-14 12:50:26.702794481 +0200 +@@ -80,4 +80,5 @@ + ghash = '' + mmp = '' + +-write_version(branch, mmp, ghash, status) ++#write_version(branch, mmp, ghash, status) ++write_version("master", None, "7baee9b8ff6e30b", "") diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb new file mode 100644 index 0000000000..9025e0fbfe --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb @@ -0,0 +1,38 @@ +name = 'PSI' +version = '4.0b6-20150814' +versionsuffix = '-mt-maxam7' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/psi4/psi4public/archive/'] +sources = ['7baee9b8ff6e30b39a7ee627750a518c39bd84f3.tar.gz'] + +patches = [ + 'PSI-%(version)s-fix-gitversion.patch', +] + +configopts = '-DLIBINT_OPT_AM=7 -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON ' + +python = 'Python' +pyver = '2.7.10' + +dependencies = [ + (python, pyver), + ('Boost', '1.58.0', '-%s-%s' % (python, pyver)), +] + +builddependencies = [ + ('CMake', '3.2.3'), + ('Perl', '5.20.1', '-bare'), # for the test suite +] + +# Execute only the 'quick' tests and run 4 in parallel +runtest = 'ARGS="-V -L quicktests -j 4 -E \'pywrap-freq-e-sowreap|stability1|libefp-qchem-qmefp-puream-sp\'" test' + +moduleclass = 'chem' -- GitLab From 0e8d44e099b0778c506574118191ddce86f89fd8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 17 Aug 2015 11:02:22 +0200 Subject: [PATCH 0836/1172] PSI-4.0b6-20150814 now with Boost 1.59 --- .../p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb index 9025e0fbfe..920ac863ac 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb @@ -24,7 +24,7 @@ pyver = '2.7.10' dependencies = [ (python, pyver), - ('Boost', '1.58.0', '-%s-%s' % (python, pyver)), + ('Boost', '1.59.0', '-%s-%s' % (python, pyver)), ] builddependencies = [ -- GitLab From 573eeb2545c8cf6ba5f23b89fdf1f7464a431765 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 11:15:43 +0200 Subject: [PATCH 0837/1172] {devel}[intel/2015a] CMake 3.3.1 --- .../c/CMake/CMake-3.3.1-intel-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb new file mode 100644 index 0000000000..b8e7064fcc --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb @@ -0,0 +1,31 @@ +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': 'intel', 'version': '2015a'} + +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' -- GitLab From 4b4643af935ccb4b3cc8eb64ce90320407eaa0f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 11:18:24 +0200 Subject: [PATCH 0838/1172] fix determining whether dependency is an external module --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a766a187d2..e45b50472c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -150,8 +150,8 @@ class EasyConfigTest(TestCase): 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['external_module']] - deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d['external_module']] + 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] -- GitLab From 6b45153d1cf9946db9191d9512b7e13f1464b151 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 17 Aug 2015 11:45:44 +0200 Subject: [PATCH 0839/1172] Newer CMake to build PSI --- .../p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb index 920ac863ac..3710c3c7c0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb @@ -28,7 +28,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.2.3'), + ('CMake', '3.3.1'), ('Perl', '5.20.1', '-bare'), # for the test suite ] -- GitLab From 38302cfbd06e54464ef62005f6156afc3b9c07a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 12:13:16 +0200 Subject: [PATCH 0840/1172] fix broken test because of change in dep_graph function --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e45b50472c..c4be112372 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -74,6 +74,7 @@ class EasyConfigTest(TestCase): 'force': True, 'optarch': 'test', 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, 'suffix_modules_path': GENERAL_CLASS, 'valid_module_classes': config.module_classes(), 'valid_stops': [x[0] for x in EasyBlock.get_steps()], @@ -124,7 +125,7 @@ class EasyConfigTest(TestCase): if self.ordered_specs is None: self.process_all_easyconfigs() - dep_graph(fn, self.ordered_specs, silent=True) + dep_graph(fn, self.ordered_specs) try: os.remove(fn) -- GitLab From 8f3d6b317454335ae913da4844819577578a79c0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 17 Aug 2015 11:46:19 +0100 Subject: [PATCH 0841/1172] Update GenomeInfoDB to 1.4.2 --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 727f3f1235..92793424b2 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -44,7 +44,7 @@ exts_list = [ ('Biobase', '2.28.0', bioconductor_options), ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.7', bioconductor_options), - ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('GenomeInfoDb', '1.4.2', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 104b0692cd..361b9b9034 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -44,7 +44,7 @@ exts_list = [ ('Biobase', '2.28.0', bioconductor_options), ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.7', bioconductor_options), - ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('GenomeInfoDb', '1.4.2', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), -- GitLab From 4ff1cad4f718bb0b56c74b736e9eec59a5e01a6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 14:04:04 +0200 Subject: [PATCH 0842/1172] fix versions for Bioconductor pkgs rtracklayer, GenomicFeatures, VariantAnnotation --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 6 +++--- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 92793424b2..9341717de6 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -81,9 +81,9 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.7', bioconductor_options), + ('rtracklayer', '1.28.8', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), + ('GenomicFeatures', '1.20.2', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -98,7 +98,7 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('BSgenome', '1.36.3', bioconductor_options), - ('VariantAnnotation', '1.14.10', bioconductor_options), + ('VariantAnnotation', '1.14.11', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.1', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 361b9b9034..a4df97360b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,9 +81,9 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.7', bioconductor_options), + ('rtracklayer', '1.28.8', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), + ('GenomicFeatures', '1.20.2', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -98,7 +98,7 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('BSgenome', '1.36.3', bioconductor_options), - ('VariantAnnotation', '1.14.10', bioconductor_options), + ('VariantAnnotation', '1.14.11', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.1', bioconductor_options), -- GitLab From c1208184a668aca8d01949f6a62a91280098d2cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 14:48:26 +0200 Subject: [PATCH 0843/1172] specify -DLIBINT_OPT_AM rather than -DLIBINT_NEW_AM, see also #1872 --- ....eb => PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb => PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb} (90%) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb similarity index 90% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb rename to easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index cf5eb269ab..d23fb6a1ea 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam8-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -1,7 +1,7 @@ name = 'PSI' version = '4.0b5' # 'maxam8': maximum angular momentum increased to 8 via LIBINT_NEW_AM -versionsuffix = '-mt-maxam8' +versionsuffix = '-mt-maxam7' homepage = 'http://www.psicode.org/' description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for @@ -32,7 +32,7 @@ dependencies = [ ('Boost', '1.59.0', pysuff), ] -# increase maximum angular momentum to 8 (specified value has to be double of the intended max!) -configopts = '-DLIBINT_NEW_AM=16' +# increase maximum angular momentum to 7 (specified value has to be double of the intended max!) +configopts = '-DLIBINT_OPT_AM=7' moduleclass = 'chem' -- GitLab From 09c652ba5c4f1c13313b2720bcca567240cf1845 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 15:01:53 +0200 Subject: [PATCH 0844/1172] fix versionsuffix to include -Python-2.7.10 --- ...PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb => PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb} (92%) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb similarity index 92% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb rename to easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb index 3710c3c7c0..c0b76dcda9 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -21,10 +21,12 @@ configopts = '-DLIBINT_OPT_AM=7 -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON ' python = 'Python' pyver = '2.7.10' +pysuff = '-%s-%s' % (python, pyver) +versionsuffix += pysuff dependencies = [ (python, pyver), - ('Boost', '1.59.0', '-%s-%s' % (python, pyver)), + ('Boost', '1.59.0', pysuff), ] builddependencies = [ -- GitLab From 3f634ae1dc7231adc1a7ddf040f0a9a0fd50afc3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 15:02:38 +0200 Subject: [PATCH 0845/1172] fix comment w.r.t. versionsuffix --- .../p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index d23fb6a1ea..f31ae0d9d8 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -1,6 +1,6 @@ name = 'PSI' version = '4.0b5' -# 'maxam8': maximum angular momentum increased to 8 via LIBINT_NEW_AM +# 'maxam7': maximum angular momentum increased to 7 via LIBINT_OPT_AM versionsuffix = '-mt-maxam7' homepage = 'http://www.psicode.org/' -- GitLab From 37605a9ace14a319ba6933d2c6f2dd3b47c32c6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Aug 2015 19:45:09 +0200 Subject: [PATCH 0846/1172] {tools}[intel/2015a] IPython 3.2.1 w/ Python 2.7.10 --- ...IPython-3.2.1-intel-2015a-Python-2.7.10.eb | 56 +++++++++++++++++++ .../libsodium/libsodium-1.0.3-intel-2015a.eb | 20 +++++++ ...Q-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb | 33 +++++++++++ .../util-linux-2.26.2-intel-2015a.eb | 33 +++++++++++ .../z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb | 35 ++++++++++++ 5 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..134d5e971e --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.1' + +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), + ('PyZMQ', '14.7.0', '%s-zmq4' % versionsuffix), +] + +# 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 = [ + ('pysqlite', '2.7.0', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/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 = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb new file mode 100644 index 0000000000..761355fc9f --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.3' + +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': '2015a'} + +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/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb new file mode 100644 index 0000000000..0c0220478e --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.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': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '4.1.3' + +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-2.26.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb new file mode 100644 index 0000000000..0d1eb341d5 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb new file mode 100644 index 0000000000..e23ec179be --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.3' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.2'), + ('libsodium', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From c3e8b99c69155cd4529e950d349f3dada5c4d548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 09:17:03 +0200 Subject: [PATCH 0847/1172] add dependencies for IPython notebook and enhance sanity check --- ...IPython-3.2.1-intel-2015a-Python-2.7.10.eb | 25 ++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb index 134d5e971e..4d65554dd4 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -24,9 +24,8 @@ 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 = [ ('pysqlite', '2.7.0', { @@ -39,8 +38,24 @@ exts_list = [ ('Pygments', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], }), + ('tornado', '4.2.1', { + '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', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('terminado', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), ('ipython', version, { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', }), ] @@ -51,6 +66,10 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], } -sanity_check_commands = [('iptest','')] +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] moduleclass = 'tools' -- GitLab From f85cb53a7cd6aae39eaf57cca0a053320e19daa4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 18 Aug 2015 10:28:08 +0200 Subject: [PATCH 0848/1172] Update gdk-pixbuf-2.31.4-intel-2015a.eb --- .../easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb index bb9b01af4f..5cb8ff5f1f 100644 --- a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GLib', '2.41.2'), ('libjpeg-turbo', '1.4.0'), - ('libpng', '1.6.16'), + ('libpng', '1.6.17'), ('LibTIFF', '4.0.3'), ] -- GitLab From cae68f086f66a64c2d1df348f874a819dfd019cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 10:34:45 +0200 Subject: [PATCH 0849/1172] add ptyprocess as dep for terminado --- .../i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb index 4d65554dd4..4c966b0d8a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -50,6 +50,9 @@ exts_list = [ ('mistune', '0.7', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), ('terminado', '0.5', { 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], }), -- GitLab From fbe668b427c418b70cfc36d1ce8e54f3cc8784cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 11:09:01 +0200 Subject: [PATCH 0850/1172] fix config option for max angular momentum --- .../p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index f31ae0d9d8..abe54f6c2d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -32,7 +32,7 @@ dependencies = [ ('Boost', '1.59.0', pysuff), ] -# increase maximum angular momentum to 7 (specified value has to be double of the intended max!) -configopts = '-DLIBINT_OPT_AM=7' +# increase maximum angular momentum to 7 +configopts = '--with-max-am-eri 7' moduleclass = 'chem' -- GitLab From 2ad351eb13e7e708db6ddea9f63ffe5b52152ede Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 11:50:10 +0200 Subject: [PATCH 0851/1172] use '=' in PSI configure option because it's stupid --- .../p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index abe54f6c2d..e299f3c676 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -33,6 +33,6 @@ dependencies = [ ] # increase maximum angular momentum to 7 -configopts = '--with-max-am-eri 7' +configopts = '--with-max-am-eri=7' moduleclass = 'chem' -- GitLab From cd203e10a877964007d8234e317cff2faf8bc5f5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 18 Aug 2015 13:18:45 +0200 Subject: [PATCH 0852/1172] Downgrade cmake version for PSI4 --- .../p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb index 3710c3c7c0..920ac863ac 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7.eb @@ -28,7 +28,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.3.1'), + ('CMake', '3.2.3'), ('Perl', '5.20.1', '-bare'), # for the test suite ] -- GitLab From d0d400a5808175796a80515be0011d2c48737969 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 14:42:02 +0200 Subject: [PATCH 0853/1172] add zlib as dep for AFNI --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index a1bc13fc57..ee50f396cf 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -36,6 +36,7 @@ dependencies = [ ('libjpeg-turbo', '1.4.0'), ('GSL', '1.16'), ('GLib', '2.40.0'), # must match version used in Qt (via PyQt) + ('zlib', '1.2.8'), ] buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver -- GitLab From c8d48355397b367e03dd6c0e1bef99a963a232ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 14:55:04 +0200 Subject: [PATCH 0854/1172] {chem}[intel/2015a] Molpro 2012.1.27 --- .../m/Molpro/Molpro-2012.1.27-intel-2015a.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb new file mode 100644 index 0000000000..bfa90c0102 --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb @@ -0,0 +1,17 @@ +name = 'Molpro' +version = '2012.1.27' + +homepage = 'https://molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# no source URL available, requires registration to download +sources = ['%(namelower)s.%(version)s.tar.gz'] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') + +moduleclass = 'chem' -- GitLab From b3f211a5a3476beb9ae0d27da41dd7b7e150d2b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 15:30:00 +0200 Subject: [PATCH 0855/1172] also define LFLAGS in list of build options for AFNI --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index ee50f396cf..bf0e2b5019 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -46,7 +46,7 @@ buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" ' +buildopts += 'LD="${CC} \$(CPROF)" LFLAGS="-L. ${LDFLAGS}" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver buildopts += 'XLIBS="-lXm -lXt"' -- GitLab From ed173b2724e523b7b21ba5c0bf776faf5e68062e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 15:56:26 +0200 Subject: [PATCH 0856/1172] define LZLIB rather than LFLAGS in AFNI build options --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index bf0e2b5019..8ea553e602 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -46,7 +46,7 @@ buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LFLAGS="-L. ${LDFLAGS}" ' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="-L${EBROOTZLIB}/lib -lz" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver buildopts += 'XLIBS="-lXm -lXt"' -- GitLab From d68210201c207afa06d4cb67a71592a661f3ba76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 16:14:18 +0200 Subject: [PATCH 0857/1172] statically link zlib --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 8ea553e602..60b9bc2eb0 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -46,7 +46,7 @@ buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="-L${EBROOTZLIB}/lib -lz" ' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver buildopts += 'XLIBS="-lXm -lXt"' -- GitLab From 3398c058d311df2dc8ff4a7ca23165bdb280bf2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Aug 2015 20:39:53 +0200 Subject: [PATCH 0858/1172] include GLib include dir in IFLAGS --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 60b9bc2eb0..24fa5e74ee 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -47,7 +47,7 @@ buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" ' -buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s" ' % majpyver +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s -I$EBROOTGLIB/lib/glib-2.0/include" ' % majpyver buildopts += 'XLIBS="-lXm -lXt"' parallel = 1 -- GitLab From 418cb5aaa725f0ece56ad8a2f526f250959c96d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Aug 2015 10:38:29 +0200 Subject: [PATCH 0859/1172] {vis}[intel/2015a] matplotlib 1.4.3 w/ Python 2.7.10 --- ...plotlib-1.4.3-intel-2015a-Python-2.7.10.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..0f1262c9db --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +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': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From 4c147b14a00664cccfb065ad4b6d15766d826433 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Aug 2015 11:40:52 +0200 Subject: [PATCH 0860/1172] {*}[dummy] Hadoop 2.6.0-cdh5.4.5-native + Spark 1.4.1 --- easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb | 22 ++++++++++++++ .../h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb | 30 +++++++++++++++++++ easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb | 23 ++++++++++++++ .../easyconfigs/p/protobuf/protobuf-2.6.1.eb | 19 ++++++++++++ easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb | 27 +++++++++++++++++ .../s/snappy/snappy-1.1.3-GCC-4.9.3.eb | 28 +++++++++++++++++ 6 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb new file mode 100644 index 0000000000..3107e6dbdf --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -0,0 +1,22 @@ +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': 'dummy', 'version': 'dummy'} + +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' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb new file mode 100644 index 0000000000..98cd20bd83 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.4.5' +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', '3.3.3'), + ('protobuf', '2.6.1'), + ('CMake', '3.3.1'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3')), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb new file mode 100644 index 0000000000..a18f09ae41 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.3.3' + +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' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb new file mode 100644 index 0000000000..e0cb785e1f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.6.1' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/google/protobuf/releases/download/v%(version)s/'] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb new file mode 100644 index 0000000000..fa568cc144 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.4.1' + +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/', +] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..1043087833 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb @@ -0,0 +1,28 @@ +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/' +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 && " + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' -- GitLab From 68c1284a1a5db5225d8b6040c8caef843e2b3081 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Aug 2015 13:14:38 +0200 Subject: [PATCH 0861/1172] downgrade protobuf to required version in Hadoop 2.6.0 easyconfig --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb index 98cd20bd83..e848ea7c2c 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb @@ -14,7 +14,7 @@ patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] builddependencies = [ ('Maven', '3.3.3'), - ('protobuf', '2.6.1'), + ('protobuf', '2.5.0'), # *must* be this version ('CMake', '3.3.1'), ('snappy', '1.1.3', '', ('GCC', '4.9.3')), ] -- GitLab From 4c07368696f92654eba013cdd84dfce7c98a84e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Aug 2015 15:06:14 +0200 Subject: [PATCH 0862/1172] {tools}[intel/2015a] pbs_python w/ Python 2.7.10 --- ..._python-4.6.0-intel-2015a-Python-2.7.10.eb | 44 +++++++++++++++++++ ...s_python-4.6.0-intel-2015a-Python-2.7.9.eb | 5 ++- .../pbs_python-4.6.0_remove-printf.patch | 34 ++++++++++++++ 3 files changed, 82 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f3e698bb5f --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb index 2b1f46d33d..ab7a722fec 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] -patches = ['pbs_python-%(version)s_CC.patch'] +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] python = 'Python' pythonver = '2.7.9' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch new file mode 100644 index 0000000000..9ac2e25c7b --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch @@ -0,0 +1,34 @@ +remove printf debug statements +see https://oss.trac.surfsara.nl/pbs_python/ticket/46 +author: Ewan Higgs (Ghent University) +Index: src/C++/pbs_wrap.cxx +=================================================================== +--- src/C++/pbs_wrap.cxx (revision 342) ++++ src/C++/pbs_wrap.cxx (working copy) +@@ -3015,7 +3015,7 @@ + allocate memory as a one block is handy for Python scripts + and fill in the next fields so it also works for the C-library + */ +- printf("basje \n"); ++ //printf("basje \n"); + ptr = (struct attrl *) malloc(number * sizeof(struct attrl)); + + prev = NULL; +@@ -3022,7 +3022,7 @@ + current = ptr + (number - 1); + for (i=0; i < number; i++) + { +- printf("constructor called\n"); ++ //printf("constructor called\n"); + current->name = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->resource = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->value = (char *) malloc(MAXNAMLEN * sizeof(char)); +@@ -3059,7 +3059,7 @@ + current = ptr + (number - 1); + for (i=0; i < number; i++) + { +- printf("constructor called\n"); ++ //printf("constructor called\n"); + current->name = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->resource = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->value = (char *) malloc(MAXNAMLEN * sizeof(char)); -- GitLab From 7e48bacbcf0b41fcc4e85cf20d73e3d86262f3a4 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 19 Aug 2015 15:58:18 +0200 Subject: [PATCH 0863/1172] Update binutils-2.25.eb Add support for ld.gold and option to build libiberty --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index aa312b1626..1e62e89ef4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -18,12 +18,19 @@ builddependencies = [('zlib', '1.2.8')] preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' +# make sure that system libraries are also considered by ld and ld.gold is also built +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', - 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +# Ensure PIC +buildopts = 'CFLAGS="-fPIC"' + +# If you require libiberty uncomment the following +#postinstallcmds = ["cp libiberty/libiberty.a %(installdir)s/lib/; cp include/libiberty.h %(installdir)s/include/", +# "mkdir %(installdir)s/info", +# "cp libiberty/libiberty.texi %(installdir)s/info/"] +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], -- GitLab From 12a7b052c0e1e1dba7bce06ebc692f2e6597170b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 19 Aug 2015 16:23:28 +0200 Subject: [PATCH 0864/1172] Update binutils-2.25.eb --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 1e62e89ef4..eb6c199b3b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -21,10 +21,8 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -# Ensure PIC -buildopts = 'CFLAGS="-fPIC"' - -# If you require libiberty uncomment the following +# If you require libiberty uncomment the following (you probably want a PIC build for linking purposes if you need libiberty): +#buildopts = 'CFLAGS="-fPIC"' #postinstallcmds = ["cp libiberty/libiberty.a %(installdir)s/lib/; cp include/libiberty.h %(installdir)s/include/", # "mkdir %(installdir)s/info", # "cp libiberty/libiberty.texi %(installdir)s/info/"] -- GitLab From d94c11f0c35323c14a9ff8d92982ac4e23947c77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Aug 2015 22:05:56 +0200 Subject: [PATCH 0865/1172] add include/glib-2.0 to $IFLAGS --- easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 24fa5e74ee..16a47719ba 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -47,7 +47,7 @@ buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" ' -buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s -I$EBROOTGLIB/lib/glib-2.0/include" ' % majpyver +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s -I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0" ' % majpyver buildopts += 'XLIBS="-lXm -lXt"' parallel = 1 -- GitLab From 0a467355c60175c38cddfe473b3ac89404b453ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 11:58:23 +0200 Subject: [PATCH 0866/1172] {lib}[intel/2015a] pandas 0.16.2 w/ Python 2.7.10 --- ...pandas-0.16.2-intel-2015a-Python-2.7.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..b006e661ec --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.16.2' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +pylibdir = "lib/python%s/site-packages/%s" % (pyshortver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, pyshortver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, pyshortver))], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 1e00e8816f41bd8250dafa18ce8c8d1ad0a349e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 14:00:04 +0200 Subject: [PATCH 0867/1172] copy Makefile, use 'make totality', specify installdir --- .../a/AFNI/AFNI-20150717-intel-2015a.eb | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb index 16a47719ba..c98e31bbfa 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'ConfigureMake' name = 'AFNI' version = '20150717' @@ -39,23 +39,27 @@ dependencies = [ ('zlib', '1.2.8'), ] -buildopts = '-f Makefile.linux_openmp_64 LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver +skipsteps = ['configure', 'install'] + +prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " +buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" ' -buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s -I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0" ' % majpyver -buildopts += 'XLIBS="-lXm -lXt"' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s ' % majpyver +buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' +buildopts += ' INSTALLDIR=%(installdir)s' parallel = 1 -files_to_copy = [(['afni'], 'bin')] +modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ['bin/afni'], + 'files': ['afni'], 'dirs': [], } -- GitLab From 586df9ca96b671f98ce245ec9fe6c6006c1c9aae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 17:38:28 +0200 Subject: [PATCH 0868/1172] add flex/Bison as build deps in binutils easyconfig --- easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb | 22 +++++++++++++++++++ .../easyconfigs/b/binutils/binutils-2.25.eb | 6 ++++- easybuild/easyconfigs/f/flex/flex-2.5.39.eb | 14 ++++++++++++ 3 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb new file mode 100644 index 0000000000..7828372bd5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.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': 'dummy', 'version': ''} + +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/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index eb6c199b3b..ff070ecb45 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -12,7 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] # zlib required, but being linked instatically, so not a runtime dep -builddependencies = [('zlib', '1.2.8')] +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('zlib', '1.2.8'), +] # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb new file mode 100644 index 0000000000..53eb8f6c78 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.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': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From ed1ff74cdd16b06194bd365c3894c5d58d40d8b8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 20 Aug 2015 17:52:00 +0200 Subject: [PATCH 0869/1172] Update binutils-2.25.eb Reluctantly removed advice on how to include a libiberty installation as part of binutils :P --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index ff070ecb45..2e9f5419fa 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -25,12 +25,6 @@ prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -# If you require libiberty uncomment the following (you probably want a PIC build for linking purposes if you need libiberty): -#buildopts = 'CFLAGS="-fPIC"' -#postinstallcmds = ["cp libiberty/libiberty.a %(installdir)s/lib/; cp include/libiberty.h %(installdir)s/include/", -# "mkdir %(installdir)s/info", -# "cp libiberty/libiberty.texi %(installdir)s/info/"] - binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { -- GitLab From 0707904c5ebba01655abc264500cde7e4aa1fbbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 19:18:12 +0200 Subject: [PATCH 0870/1172] fix installation prefix for SIP --- .../s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 10 +++++++++- .../s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 10 +++++++++- .../s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 10 +++++++++- .../s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 10 +++++++++- 4 files changed, 36 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 20ee0d6828..ff7096e1dd 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index 2de546ee64..fb132a3e82 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index e745733edd..a58036737a 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index 87b18fbf3c..0aa4273c0e 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' -- GitLab From 53fed9e00dc1b12cb77979231af165dd8c52b9bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 19:55:52 +0200 Subject: [PATCH 0871/1172] sync binutils 2.25 easyconfigs to enable ld.gold --- .../Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb | 22 +++++++++++ .../Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb | 22 +++++++++++ .../Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb | 22 +++++++++++ .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 8 ++-- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 13 +++++-- .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 39 +++++++++++++++++++ .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 8 ++-- .../easyconfigs/b/binutils/binutils-2.25.eb | 2 +- .../flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 15 +++++++ .../flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 15 +++++++ .../flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 15 +++++++ .../m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb | 23 +++++++++++ .../m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb | 23 +++++++++++ .../m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb | 23 +++++++++++ 14 files changed, 239 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..937ab27cb4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.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': 'GCC', 'version': '4.9.2-binutils-2.25'} + +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/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..6ab1ff9e26 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +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/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..980cf1f23c --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +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/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 6b906969bb..73f180b419 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 @@ -12,6 +12,8 @@ sources = [SOURCE_TAR_GZ] 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', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils @@ -22,10 +24,10 @@ builddependencies = [ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' +# make sure that system libraries are also considered by ld and ld.gold is also built +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 3b30b6d478..4c56a693ea 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -12,16 +12,21 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] # zlib required, but being linked instatically, so not a runtime dep -builddependencies = [('zlib', '1.2.8')] +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' +# make sure that system libraries are also considered by ld and ld.gold is also built +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..6ebb5e9803 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld and ld.gold is also built +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index e8d57cd578..369036e21b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -12,6 +12,8 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils @@ -22,10 +24,10 @@ builddependencies = [ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' +# make sure that system libraries are also considered by ld and ld.gold is also built +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' -binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 2e9f5419fa..c308c47ffd 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,10 +11,10 @@ toolchain = {'name': 'dummy', 'version': ''} 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', '1.2.8'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..62d2b642fa --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '4.9.2-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..476d76ae02 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..636806c077 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb new file mode 100644 index 0000000000..cda34c1fdb --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.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': 'GCC', 'version': '4.9.2-binutils-2.25'} + +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/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb new file mode 100644 index 0000000000..e51d2c83e7 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +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/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb new file mode 100644 index 0000000000..2c57d81600 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b7be6df150b03adab557bf184b958fbddd6d4b77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 20:42:10 +0200 Subject: [PATCH 0872/1172] fix typo in M4 easyconfigs filename --- easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb | 5 +++++ ...-binutis-2.25.eb => M4-1.4.17-GCC-4.9.2-binutils-2.25.eb} | 0 ...-binutis-2.25.eb => M4-1.4.17-GCC-4.9.3-binutils-2.25.eb} | 0 ...-binutis-2.25.eb => M4-1.4.17-GCC-5.1.0-binutils-2.25.eb} | 0 4 files changed, 5 insertions(+) rename easybuild/easyconfigs/m/M4/{M4-1.4.17-GCC-4.9.2-binutis-2.25.eb => M4-1.4.17-GCC-4.9.2-binutils-2.25.eb} (100%) rename easybuild/easyconfigs/m/M4/{M4-1.4.17-GCC-4.9.3-binutis-2.25.eb => M4-1.4.17-GCC-4.9.3-binutils-2.25.eb} (100%) rename easybuild/easyconfigs/m/M4/{M4-1.4.17-GCC-5.1.0-binutis-2.25.eb => M4-1.4.17-GCC-5.1.0-binutils-2.25.eb} (100%) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index b6d3efe3ac..ce67806f88 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -17,4 +17,9 @@ sources = ['%(namelower)s-%(version)s.gem'] dependencies = [('Ruby', rubyver)] +sanity_check_paths = { + 'files': ['bin/fpm'], + 'dirs': [], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutis-2.25.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutis-2.25.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutis-2.25.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb -- GitLab From 2ffb90c875b24575f0131afbe3ac45480c986ec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 21:19:52 +0200 Subject: [PATCH 0873/1172] don't touch the FPM easyconfig --- easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index ce67806f88..b6d3efe3ac 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -17,9 +17,4 @@ sources = ['%(namelower)s-%(version)s.gem'] dependencies = [('Ruby', rubyver)] -sanity_check_paths = { - 'files': ['bin/fpm'], - 'dirs': [], -} - moduleclass = 'tools' -- GitLab From bd8a309ae6d81254c985772e35a801752d914c6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 21:54:58 +0200 Subject: [PATCH 0874/1172] add sanity check paths for FPM --- easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index b6d3efe3ac..52783b2be4 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -17,4 +17,9 @@ sources = ['%(namelower)s-%(version)s.gem'] dependencies = [('Ruby', rubyver)] +sanity_check_paths = { + 'files': ['bin/fpm'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + moduleclass = 'tools' -- GitLab From 45f7544f29c134c74aa147bd3c25d715fb9f9aeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Aug 2015 22:12:24 +0200 Subject: [PATCH 0875/1172] add binutils build dep in M4, flex, Bison easyconfigs --- .../b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb | 6 +++++- .../b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb | 9 ++++++++- .../b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb | 6 +++++- .../f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 3 +++ .../f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 3 +++ .../f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 3 +++ .../m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 3 +++ .../m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 3 +++ .../m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 3 +++ 9 files changed, 36 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb index 937ab27cb4..41f43d9b03 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17')] +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb index 6ab1ff9e26..b5389900eb 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb @@ -12,7 +12,14 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17')] +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb index 980cf1f23c..128617a43c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17')] +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index 62d2b642fa..55d2930dcc 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -12,4 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 476d76ae02..1d773d362f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -12,4 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index 636806c077..b6406b3fee 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -12,4 +12,7 @@ toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' 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 cda34c1fdb..a79d153988 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 @@ -13,6 +13,9 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} 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 = { 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 e51d2c83e7..89984f9baf 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 @@ -13,6 +13,9 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} 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 = { 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 2c57d81600..e856a3fd43 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 @@ -13,6 +13,9 @@ toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} 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 = { -- GitLab From c8bf0f90e9e01887fcac08954110b681103d15f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 11:44:34 +0200 Subject: [PATCH 0876/1172] use --enable-plugins along with --enable-gold --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 3 ++- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 3 ++- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 3 ++- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 3 ++- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 3 ++- 5 files changed, 10 insertions(+), 5 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 73f180b419..82d314f4eb 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 @@ -25,7 +25,8 @@ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 4c56a693ea..5e6cdd8034 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -24,7 +24,8 @@ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 6ebb5e9803..2df030c239 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -25,7 +25,8 @@ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 369036e21b..25962accc2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -25,7 +25,8 @@ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld and ld.gold is also built -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' +# --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html +configopts = '--with-sysroot=/ --enable-gold --enable-ld=default --enable-plugins' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index c308c47ffd..b2c4f75fab 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -23,7 +23,8 @@ preconfigopts = 'LIBS="$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 -configopts = '--with-sysroot=/ --enable-gold --enable-ld=default ' +# --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' ] -- GitLab From cbb9da553bdfadc4f2ad25c928cd655315b80a88 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 21 Aug 2015 12:33:47 +0200 Subject: [PATCH 0877/1172] Update Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb Typo that left in line --- .../easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb index b5389900eb..333050d114 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb @@ -18,9 +18,6 @@ builddependencies = [ ('binutils', '2.25', '', True), ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] - sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], 'dirs': [], -- GitLab From 335d57ca669d42caa615afe364480bd28d7504fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 13:35:04 +0200 Subject: [PATCH 0878/1172] fix include path for SIP --- .../easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 4 ++-- .../easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 4 ++-- .../easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 4 ++-- .../easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index ff7096e1dd..2c2c1d2e6a 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -21,11 +21,11 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[:2]) -configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver sanity_check_paths = { - 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + 'files': ['bin/sip', 'include/sip.h'] + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index fb132a3e82..db47a517ca 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -21,11 +21,11 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[:2]) -configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver sanity_check_paths = { - 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + 'files': ['bin/sip', 'include/sip.h'] + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index a58036737a..c03c93c847 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -21,11 +21,11 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[:2]) -configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver sanity_check_paths = { - 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + 'files': ['bin/sip', 'include/sip.h'] + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index 0aa4273c0e..4fb9048408 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -21,11 +21,11 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[:2]) -configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include/python%s " % pyshortver +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver sanity_check_paths = { - 'files': ['bin/sip', 'include/python%s/sip.h' % pyshortver] + + 'files': ['bin/sip', 'include/sip.h'] + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } -- GitLab From 74e322855f71ce015b1aebf9ac31d15b6247fc9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 13:51:25 +0200 Subject: [PATCH 0879/1172] include GMP dep in Python 2.7.10 easyconfig --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 8d705315cc..45878617c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -22,6 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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 2f2456737857a5d30f8a337d4f44c36996456190 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 13:52:30 +0200 Subject: [PATCH 0880/1172] {math}[GNU/4.9.3-2.25] GMP 6.0.0a --- .../g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..692f1fd842 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 5aa43d5ed716fbd745802e02493b2f31396a7455 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 15:39:12 +0200 Subject: [PATCH 0881/1172] add custom sanity check paths for PyQt --- .../p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 13 +++++++++---- .../p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb | 13 +++++++++---- .../p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb | 13 +++++++++---- .../p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb | 13 +++++++++---- 4 files changed, 36 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 35c97630e9..ef867422c5 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb index aab3898aa9..48c5bb750a 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb index 34baa22804..992e13df88 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb index 789bf13b2c..f40c0f4c4b 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' -- GitLab From 98e33b97fdfe9a558160ec951e4e28727a221ef2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Aug 2015 23:27:24 +0200 Subject: [PATCH 0882/1172] more Bioconductor pkg version bumps --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 6 +++--- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 9341717de6..db382cbce8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -48,7 +48,7 @@ exts_list = [ ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.3', bioconductor_options), + ('Biostrings', '2.36.4', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -81,9 +81,9 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.8', bioconductor_options), + ('rtracklayer', '1.28.9', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), - ('GenomicFeatures', '1.20.2', bioconductor_options), + ('GenomicFeatures', '1.20.3', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index a4df97360b..dd15792423 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -48,7 +48,7 @@ exts_list = [ ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.3', bioconductor_options), + ('Biostrings', '2.36.4', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -81,9 +81,9 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), - ('rtracklayer', '1.28.8', bioconductor_options), + ('rtracklayer', '1.28.9', bioconductor_options), ('biomaRt', '2.24.0', bioconductor_options), - ('GenomicFeatures', '1.20.2', bioconductor_options), + ('GenomicFeatures', '1.20.3', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), -- GitLab From e7cf951a9f481b2bbc65abe4aa3f970e5e66903a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 22 Aug 2015 09:04:43 +0100 Subject: [PATCH 0883/1172] Update Xerces to 3.1.2 --- .../Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb | 20 +++++++++++++++++++ .../Xerces-C++-3.1.2-intel-2015a.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb new file mode 100644 index 0000000000..78cd8b676c --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' +description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/3/sources/' +] + +dependencies = [ + ('cURL', '7.40.0'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb new file mode 100644 index 0000000000..fe21515dfe --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' +description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/3/sources/' +] + +dependencies = [ + ('cURL', '7.40.0'), +] + +moduleclass = 'lib' -- GitLab From 0313c2e0b0446a6dfd582b423461c04332156b47 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 22 Aug 2015 09:18:01 +0100 Subject: [PATCH 0884/1172] Update Xerces cURL dependency to 7.44.0 --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb index 78cd8b676c..e17a7801f2 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -14,7 +14,7 @@ source_urls = [ ] dependencies = [ - ('cURL', '7.40.0'), + ('cURL', '7.44.0'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb index fe21515dfe..c783310ea2 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ source_urls = [ ] dependencies = [ - ('cURL', '7.40.0'), + ('cURL', '7.44.0'), ] moduleclass = 'lib' -- GitLab From af7ec5d858af02315bd635e4e930de19649eaace Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 23 Aug 2015 07:21:47 +0100 Subject: [PATCH 0885/1172] Update cURL to 7.44.0 --- .../c/cURL/cURL-7.44.0-foss-2015a.eb | 31 +++++++++++++++++++ .../c/cURL/cURL-7.44.0-goolf-1.7.20.eb | 31 +++++++++++++++++++ .../c/cURL/cURL-7.44.0-intel-2015a.eb | 31 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb new file mode 100644 index 0000000000..19e23c5058 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +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': 'foss', 'version': '2015a'} + +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.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..22021b62b5 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +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': 'goolf', 'version': '1.7.20'} + +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=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb new file mode 100644 index 0000000000..4957904abe --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 4981d5b2b8fed5374a37eb1a1fda048bf3e65069 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 11:07:26 +0200 Subject: [PATCH 0886/1172] add custom sanity check paths in mpi4py easyconfigs --- .../m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 6 ++++++ .../m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 6 ++++++ 7 files changed, 42 insertions(+) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 832a044412..98f6b375df 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index d7ce479c30..58e1efec95 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb index f3694ef966..8d1017dab1 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -24,4 +24,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index 52e2739364..fff549de1f 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index 5878a3a0a6..9fe2a5f319 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 989b264cf7..eaf599c8ab 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -21,4 +21,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 6f9b95ae80..07635c8d39 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -21,4 +21,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' -- GitLab From 96cffbb38d6929bc548f09eb8580a7cbc4d7266c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 11:08:33 +0200 Subject: [PATCH 0887/1172] add custom sanity check paths in YAML-Syck easyconfigs --- .../y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 5 +++++ .../y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb | 5 +++++ .../y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 5 +++++ 3 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 587b16d748..a3a8d2e338 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -32,4 +32,9 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index a394ff11d0..2133f05c4e 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -32,4 +32,9 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 94ef6fae9e..91c7893f0d 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -32,4 +32,9 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], +} + moduleclass = 'data' -- GitLab From 1232d8def92d2b46970376af973d373ff4fe3e2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 11:11:28 +0200 Subject: [PATCH 0888/1172] don't hardcode Perl version in YAML-Syck sanity check paths --- .../y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 3 ++- .../y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb | 3 ++- .../y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index a3a8d2e338..b409a46b6b 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -32,9 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index 2133f05c4e..fa45b910fb 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -32,9 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 91c7893f0d..f2c952182b 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -32,9 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/5.16.3/x86_64-linux-thread-multi/YAML'], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], } moduleclass = 'data' -- GitLab From 7b10f50908c85d00b848ea583a2765ba0a73e3aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 12:27:51 +0200 Subject: [PATCH 0889/1172] add custom sanity check paths in Perl XML easyconfigs --- .../x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb | 6 ++++++ .../x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb | 6 ++++++ .../x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb index 744de7be27..876f399a73 100644 --- a/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'XML::Dumper'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/XML/Dumper.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb index 5248d49efa..fe8c2f1f48 100644 --- a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Parser'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/XML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb index 95ee785c73..7e5833d70b 100644 --- a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Parser'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/XML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb index acd24ee883..b28c4775b7 100644 --- a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Twig'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['bin/xml_grep', 'bin/xml_merge', 'bin/xml_pp', 'bin/xml_spellcheck', 'bin/xml_split'], + 'dirs': ['lib/perl%s/site_perl/%s/XML/Twig' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb index 41318259ee..72f33a067d 100644 --- a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Twig'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['bin/xml_grep', 'bin/xml_merge', 'bin/xml_pp', 'bin/xml_spellcheck', 'bin/xml_split'], + 'dirs': ['lib/perl%s/site_perl/%s/XML/Twig' % (perlmajver, perlver)], +} + moduleclass = 'data' -- GitLab From a8549b4d185c3154f5d7f77f700f0e1a09e4e203 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 12:28:36 +0200 Subject: [PATCH 0890/1172] add custom sanity check paths in R XML easyconfigs --- .../XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb | 13 +++++++++---- .../x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb | 5 +++++ .../x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb | 13 +++++++++---- .../x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb | 13 +++++++++---- 4 files changed, 32 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb index dfbf3d0849..f9b761e2bb 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb @@ -18,11 +18,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb index 366fa8a2aa..e2975b9958 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb @@ -22,4 +22,9 @@ dependencies = [ options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb index 695f7960bc..41f30ad32d 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb @@ -18,11 +18,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb index e5358dc0d2..628ddd6ba4 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb @@ -16,11 +16,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' -- GitLab From 3acd4c121a6516e9aabcc9c22388845b367fc1df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 23 Aug 2015 11:34:39 +0100 Subject: [PATCH 0891/1172] Fix long lines in Xerces description --- .../x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb | 7 ++++++- .../x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb index e17a7801f2..801f0ca105 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -4,7 +4,12 @@ name = 'Xerces-C++' version = '3.1.2' homepage = 'http://xerces.apache.org/xerces-c/' -description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb index c783310ea2..c6c6bc70ec 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -4,7 +4,12 @@ name = 'Xerces-C++' version = '3.1.2' homepage = 'http://xerces.apache.org/xerces-c/' -description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From cc2138cc043e1488977c74f43d29effc90999afd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 14:16:17 +0200 Subject: [PATCH 0892/1172] add custom sanity check paths in vsc-processcontrol and vsc-mympirun-scoop easyconfigs --- .../vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 5 +++++ .../v/vsc-processcontrol/vsc-processcontrol-1.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index c1d224e11e..dfd259613d 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -24,4 +24,9 @@ dependencies = [ options = {'modulename': 'vsc.mympirun.scoop'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/mympirun/scoop'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb index 2b715acacf..e6b6aa4d74 100644 --- a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb @@ -17,4 +17,9 @@ dependencies = [('vsc-base', '1.7.3')] options = {'modulename': 'sys; print sys.path; import vsc; print vsc.__path__; import vsc.processcontrol'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/processcontrol'], +} + moduleclass = 'tools' -- GitLab From d5e107690cbac786b28a6b6dac2cd19ae7adc3f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 14:17:24 +0200 Subject: [PATCH 0893/1172] add custom sanity check paths in GraphViz Perl easyconfigs --- .../g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 7 ++++++- .../g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb index a7968a4929..4dc6df7462 100644 --- a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -21,7 +21,12 @@ dependencies = [ ("Graphviz", "2.38.0"), ] - options = {'modulename': 'GraphViz'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/GraphViz.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/GraphViz' % (perlmajver, perlver)], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb index 0165dca509..aa178c12fe 100644 --- a/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb @@ -21,7 +21,12 @@ dependencies = [ ("Graphviz", "2.38.0"), ] - options = {'modulename': 'GraphViz2'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/GraphViz2.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/GraphViz2' % (perlmajver, perlver)], +} + moduleclass = 'vis' -- GitLab From c627d8c23612fecf09289cd746c886898c7444fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 14:44:48 +0200 Subject: [PATCH 0894/1172] add custom sanity check paths in scikit-learn easyconfigs --- ...n-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 23 +++++++++++------- ...it-learn-0.13-ictce-4.1.13-Python-2.7.3.eb | 24 ++++++++++++------- ...kit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb | 24 ++++++++++++------- ...it-learn-0.14-ictce-4.1.13-Python-2.7.5.eb | 23 +++++++++++------- ...kit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb | 23 +++++++++++------- ...kit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb | 23 +++++++++++------- ...t-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 15 ++++++++---- 7 files changed, 96 insertions(+), 59 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 96310147cf..2a0f4d4d18 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.13" +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,15 +14,20 @@ toolchain = {'version': '1.1.0-no-OFED', 'name': 'goalf'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:2]) +python = 'Python' +pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.1.1', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb index 568e256fdc..4c9a59e090 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb @@ -1,6 +1,7 @@ -easyblock = "PythonPackage" -name = "scikit-learn" -version = "0.13" +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -13,15 +14,20 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.2.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb index e7e1f0c322..59b7700e6f 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb @@ -1,6 +1,7 @@ -easyblock = "PythonPackage" -name = "scikit-learn" -version = "0.13" +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -13,15 +14,20 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.2.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb index 202d34e111..839a8322ab 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb index 380fb7075a..5570f2d348 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb index 22f760cf88..8d66e69020 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.6' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.6' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.1', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb index 8b997036dd..0a1c8f2b9c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -15,15 +15,20 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:-1]) -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.4.3', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], +} moduleclass = 'data' -- GitLab From df2114bbb07ae3b114ba8685d71e04c7576608d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 15:14:12 +0200 Subject: [PATCH 0895/1172] add custom sanity check paths in paycheck easyconfigs --- .../paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++++++ .../p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 6 ++++++ .../p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb | 6 ++++++ .../p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb | 6 ++++++ .../p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 05e281d1d7..2d44a2d96b 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 67f7bc47b5..67abbe4783 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -18,4 +18,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb index 0f1fade586..14fdb01611 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 5170a4d2bd..9fdde70731 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb index f140852405..dcddbf5da1 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' -- GitLab From 3faebe77772946c0f99c2180242a8687f09ac260 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 15:18:03 +0200 Subject: [PATCH 0896/1172] fix typo in scikit-learn easyconfigs --- .../scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 4 ++-- .../scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb | 4 ++-- .../scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb | 4 ++-- .../scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb | 4 ++-- .../scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2a0f4d4d18..fcb7b2818b 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.3' -pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -25,9 +24,10 @@ dependencies = [ ] options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb index 4c9a59e090..1323b9230c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.3' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -25,9 +24,10 @@ dependencies = [ ] options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb index 59b7700e6f..5cce29e1ea 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.3' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -25,9 +24,10 @@ dependencies = [ ] options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb index 839a8322ab..0ca848e977 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -26,9 +25,10 @@ dependencies = [ options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb index 5570f2d348..3f7d9ba4f7 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.5' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -26,9 +25,10 @@ dependencies = [ options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb index 8d66e69020..8ef7bdd7ea 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.6' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -26,9 +25,10 @@ dependencies = [ options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb index 0a1c8f2b9c..ea3aa7a366 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' -pyshortver = '.'.join(pyver.split('.')[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ @@ -26,9 +25,10 @@ dependencies = [ options = {'modulename': 'sklearn'} +pyshortver = '.'.join(pyver.split('.')[:-1]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/sklearn' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], } moduleclass = 'data' -- GitLab From b6ae841fa1616292342e8869cb974500f6aae0e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 16:15:40 +0200 Subject: [PATCH 0897/1172] add custom sanity check paths in MDP easyconfigs --- .../MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 15 ++++++++++----- .../m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb | 15 ++++++++++----- .../m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb | 15 ++++++++++----- .../m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb | 15 ++++++++++----- 4 files changed, 40 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 3818ea1e1b..ebdb88d2e4 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb index e0c5549352..d72a56800d 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb index ecbabdb002..97479dc022 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb index 007fc91caa..5538ab064d 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb @@ -14,12 +14,17 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' -- GitLab From 19ad179dfe2817fc481c86aa1c952bd480bde016 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 16:27:40 +0200 Subject: [PATCH 0898/1172] add custom sanity check paths in ncdf + ncdf4 R easyconfigs --- .../easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb | 5 +++++ .../easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb | 5 +++++ .../n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb | 5 +++++ .../easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb | 5 +++++ .../easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 5 +++++ .../n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb | 5 +++++ .../easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb | 5 +++++ 7 files changed, 35 insertions(+) diff --git a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb index a5891cb70a..ba779e4d32 100644 --- a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb +++ b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1', '-zlib-1.2.5'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb index dc58f15fe2..92ad89bc5d 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1', '-zlib-1.2.5'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb index 0f47ffdcef..420a463745 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb @@ -27,4 +27,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb index 20417f1a1f..e2d4470245 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index 47cf63ba0e..93af22628c 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -24,4 +24,9 @@ dependencies = [ ('cURL', '7.37.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb index 491a03c606..4ef7a218bc 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb @@ -27,4 +27,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb index 17bf529b5e..ab54113dcc 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' -- GitLab From 14ce83af732935879b1a3936b77201ac4c75d3e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 17:15:53 +0200 Subject: [PATCH 0899/1172] add custom sanity check paths in various easyconfigs for R libraries --- .../AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb | 13 +++++++++---- .../AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb | 13 +++++++++---- .../e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb | 5 +++++ .../e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb | 5 +++++ .../f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb | 13 +++++++++---- .../f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb | 13 +++++++++---- .../f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb | 5 +++++ .../g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb | 5 +++++ .../r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb | 7 ++++++- .../runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb | 7 ++++++- 10 files changed, 68 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb index cb3b9b70fd..809adaa54b 100644 --- a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb @@ -19,9 +19,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnalyzeFMRI'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb index b66dfc2b4c..530418299d 100644 --- a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb @@ -20,9 +20,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnalyzeFMRI'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb index ffb121f546..2b79d60ce9 100644 --- a/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb @@ -24,4 +24,9 @@ dependencies = [ ('gsl', '1.9-10', versionsuffix), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb index ee1750e53d..b3a13971b3 100644 --- a/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb @@ -24,4 +24,9 @@ dependencies = [ ('gsl', '1.9-10', versionsuffix), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb index 4cec82a9a5..af9a94344b 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb @@ -21,9 +21,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb index 6d1befc47f..ebe8dc05d0 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb @@ -21,9 +21,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb index dacaf55d84..b6097690db 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb @@ -26,4 +26,9 @@ dependencies = [ ('Tk', tcltkver), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb index 616d9c3020..36d3ba6863 100644 --- a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb @@ -21,4 +21,9 @@ dependencies = [ ('GSL', '1.16'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['gsl'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb index 20b52d9cda..8ed75f2aca 100644 --- a/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb @@ -20,7 +20,12 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ("JAGS", "3.4.0"), + ('JAGS', '3.4.0'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb index 23eb067771..f7c90f5eff 100644 --- a/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb @@ -20,7 +20,12 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ("JAGS", "3.4.0"), + ('JAGS', '3.4.0'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['runjags'], +} + moduleclass = 'math' -- GitLab From ae72e902ea9629f1a29769ab3b5aeb24a18b3a45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 17:17:55 +0200 Subject: [PATCH 0900/1172] add custom sanity check paths in various easyconfigs for Python packages --- .../Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 16 ++++++++++------ .../Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb | 16 ++++++++++------ .../bibtexparser-0.5-foss-2015a-Python-2.7.9.eb | 6 ++++++ ...bibtexparser-0.5-intel-2015a-Python-2.7.9.eb | 6 ++++++ ...ibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb | 6 ++++++ ...btexparser-0.6.0-intel-2015a-Python-2.7.9.eb | 6 ++++++ ...netifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 13 +++++++++---- .../netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb | 13 +++++++++---- .../networkx-1.10-intel-2015a-Python-2.7.10.eb | 6 ++++++ .../networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 6 ++++++ ...ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb | 17 +++++++++++------ .../PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb | 12 +++++++++--- .../Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb | 15 ++++++++++----- .../pycosat-0.6.0-intel-2015a-Python-2.7.10.eb | 6 ++++++ ...graphviz-1.3rc2-intel-2015a-Python-2.7.10.eb | 6 ++++++ .../rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb | 6 ++++++ .../rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb | 6 ++++++ 17 files changed, 128 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 46e8bcb1a8..bcb87d2e39 100644 --- a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -11,12 +11,16 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -pylibdir = 'lib/python%s/site-packages' % pythonshortver -versionsuffix = '-%s-%s' % (python, pythonver) +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pythonver)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/biggus' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb index 4374be186c..c1cac11dcc 100644 --- a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -11,12 +11,16 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -pylibdir = 'lib/python%s/site-packages' % pythonshortver -versionsuffix = '-%s-%s' % (python, pythonver) +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pythonver)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/biggus' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb index 383c7de16a..2ec986e1f9 100644 --- a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb @@ -17,4 +17,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb index 4c591a3fc0..43af690ca6 100644 --- a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb @@ -17,4 +17,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb index 7060a6e07d..0473d2694f 100644 --- a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb @@ -17,4 +17,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb index 88ee53e88a..0cf333f02a 100644 --- a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb @@ -17,4 +17,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index 26cfac901b..bd3aec85fa 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -14,14 +14,19 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] options = {'modulename': 'netifaces'} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], + 'dirs': [], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb index 7994c5fb6e..c636b30fb5 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb @@ -14,14 +14,19 @@ source_urls = ['http://alastairs-place.net/projects/netifaces/'] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.6' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.6' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] options = {'modulename': 'netifaces'} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], + 'dirs': [], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb index 648339c9c8..422e3c8940 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb @@ -20,4 +20,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb index f6ae1e74b7..718e562799 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -21,4 +21,10 @@ dependencies = [ (python, pythonver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb index a404ae249a..28dbe78fdb 100644 --- a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'ordereddict' version = '1.1' @@ -13,12 +13,17 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://pypi.python.org/packages/source/o/%(namelower)s'] sources = [SOURCELOWER_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/ordereddict.py' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb index a42bb5b4d8..1c5dde3609 100644 --- a/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb @@ -18,11 +18,11 @@ sources = [SOURCE_TAR_GZ] patches = ['PyQuante-1.6.4-Libint.patch'] python = 'Python' -pythonver = '2.7.5' -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ('numpy', '1.8.0', versionsuffix), ('matplotlib', '1.3.1', versionsuffix), ('Libint', '1.1.4'), @@ -30,4 +30,10 @@ dependencies = [ options = {'modulename': name} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb index 2453963f18..d24209c2d9 100644 --- a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -13,16 +13,21 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_ZIP] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('numpy','1.6.2', versionsuffix), ('scipy', '0.11.0', versionsuffix), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/pyke' % pyshortver], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb index b8c14278d8..0dcfa43ff4 100644 --- a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb @@ -20,4 +20,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pycosat.so' % pyshortver], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb index ba6e1cf97c..1804c2f2a8 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb @@ -21,4 +21,10 @@ dependencies = [ ('Graphviz', '2.38.0', versionsuffix), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pygraphviz' % pyshortver], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb index aeaed8d595..463de39baa 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -15,6 +15,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -22,4 +23,9 @@ dependencies = [ ('R', '2.15.2'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb index 6d5edb8ec2..5287791d7c 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -15,6 +15,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '3.2.3' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -22,4 +23,9 @@ dependencies = [ ('R', '2.15.2'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'mpi' -- GitLab From e1e2752f026e50b3d64f1df8f6018c51124ae759 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 17:18:55 +0200 Subject: [PATCH 0901/1172] add custom sanity check paths in various easyconfigs for Perl modules --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb | 6 ++++++ .../d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb | 6 ++++++ .../g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb | 6 ++++++ .../n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb | 7 ++++++- .../Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb | 6 ++++++ .../s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb | 5 +++++ 9 files changed, 53 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index facf14e7e4..55ffd3cd6a 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -22,4 +22,10 @@ dependencies = [ options = {'modulename': 'DBD::Pg'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/Pg.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb index 318f3d639e..c8b287035b 100644 --- a/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'DBD::SQLite'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/SQLite.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/SQLite' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb index 2bcf9d9a0e..b518ac35ed 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb @@ -22,4 +22,10 @@ dependencies = [ options = {'modulename': 'DBD::mysql'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index 3aa72fb22a..bdcb00e69d 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -21,4 +21,10 @@ dependencies = [ (perl, perlver), ] +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index 3636f4ea5c..831d1e8494 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ (perl, perlver), ] +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb index fc5eb6da7b..96fa7554f4 100644 --- a/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'GSSAPI'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/GSSAPI.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/GSSAPI' % (perlmajver, perlver)], +} + moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb index e208935ff8..0dbda2b162 100644 --- a/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb @@ -23,5 +23,10 @@ dependencies = [ options = {'modulename': 'Net::LibIDN'} -moduleclass = 'system' +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Net/LibIDN.pm' % (perlmajver, perlver)], + 'dirs': [], +} +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb index b35839d741..973a23b9d2 100644 --- a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -30,4 +30,10 @@ dependencies = [ options = {'modulename': 'Parallel::ForkManager'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/Parallel/ForkManager.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb index e58e9e902a..cf5f1f9a02 100644 --- a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb @@ -19,4 +19,9 @@ versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [('GraphViz', '2.18', versionsuffix)] +sanity_check_paths = { + 'files': ['bin/SOBAcl', 'bin/so_tree', 'lib/Bundle/SOBA.pm', 'lib/SOBA/Base.pm', 'lib/SOBA/Run.pm'], + 'dirs': [], +} + moduleclass = 'bio' -- GitLab From 8264cbf956b1d4b535f278d2249b840b472be87a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 17:35:09 +0200 Subject: [PATCH 0902/1172] fix typo in networkx easyconfig --- .../n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb index 718e562799..bedaf28b91 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -13,12 +13,12 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] pyshortver = '.'.join(pyver.split('.')[:2]) -- GitLab From 727c774993d26f15ca120e2414353b5554f06690 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 18:04:35 +0200 Subject: [PATCH 0903/1172] fix typo in FastTree and fastqz easyconfigs --- easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb index 67920d1a2d..3352880d36 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb index b7b0c00339..7447f915f3 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 7bcbad6706..902b240c04 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -30,7 +30,7 @@ dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] cmds_map = [ - ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %%(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') ] -- GitLab From ef9b185df938331f6c26b037fb76e884e9d4a38d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 18:26:09 +0200 Subject: [PATCH 0904/1172] fix sanity check in easyconfig for Biggues 0.11.0 --- .../b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb index bcb87d2e39..c3067d5644 100644 --- a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -20,7 +20,7 @@ dependencies = [(python, pyver)] pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/biggus' % pyshortver], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], } moduleclass = 'data' -- GitLab From 90ddffa34342bd30bb3a46471283d542939d013c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Aug 2015 19:45:24 +0200 Subject: [PATCH 0905/1172] don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig --- .../SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb index 267fa3a4ce..ace5e25985 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb @@ -5,7 +5,7 @@ homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -- GitLab From cc34b7d1cb588ec76eed9d9af53fad849b5700df Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 24 Aug 2015 09:31:20 +0200 Subject: [PATCH 0906/1172] GMT update --- .../g/GDAL/GDAL-2.0.0-intel-2015a.eb | 29 +++++++++ .../g/GMT/GMT-5.1.0-goolf-1.4.10.eb | 8 ++- .../g/GMT/GMT-5.1.2-intel-2015a.eb | 61 +++++++++++++++++++ .../easyconfigs/g/GMT/GMT-5.1.2_netCDF.patch | 23 +++++++ .../n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 32 ++++++++++ 5 files changed, 152 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GMT/GMT-5.1.2_netCDF.patch create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb new file mode 100644 index 0000000000..fbe76fab64 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.0.0' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.3.3.1'), + ('expat', '2.1.0'), + ('libxml2', '2.9.2', '-Python-2.7.9'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb index df5338ee11..8ac6f24179 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb @@ -13,7 +13,13 @@ description = """GMT is an open source collection of about 80 command-line tools toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = ['gmt-%(version)s-src.tar.bz2'] -source_urls = ['http://gmt.soest.hawaii.edu/files/download?name='] +# http download requires flash enabled browser +#http://gmt.soest.hawaii.edu/files/download?name= +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gmt/legacy', +] + builddependencies = [('CMake', '2.8.11')] diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb new file mode 100644 index 0000000000..8f2f3a4f84 --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb @@ -0,0 +1,61 @@ +name = "GMT" +version = "5.1.2" + +easyblock = "CMakeMake" + +homepage = 'http://gmt.soest.hawaii.edu/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +gshhg_ver = '2.3.4' +dcw_ver = '1.1.1' +sources = [ + 'gmt-%(version)s-src.tar.bz2', + #coastlines, rivers, and political boundaries + 'gshhg-gmt-%s.tar.gz' % gshhg_ver, + #country polygons + 'dcw-gmt-%s.tar.gz' % dcw_ver, +] + +#'http://gmt.soest.hawaii.edu/files/download?name=' needs flash enabled browser +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gmt/legacy', + 'ftp://ftp.soest.hawaii.edu/gshhg', + 'ftp://ftp.soest.hawaii.edu/gshhg/legacy', + 'ftp://ftp.soest.hawaii.edu/dcw', + 'ftp://ftp.soest.hawaii.edu/dcw/legacy', +] + +patches = ['GMT-5.1.2_netCDF.patch'] + +builddependencies = [('CMake', '3.2.2')] + +dependencies = [ + ('PCRE', '8.37'), + ('GDAL', '2.0.0'), + ('FFTW', '3.3.4'), + ('netCDF', '4.3.3.1'), + ('Ghostscript', '9.16'), +] + +configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % gshhg_ver +configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % dcw_ver +#configopts = "-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=/tmp/hajgato/build/GMT/5.1.2/intel-2015a/gshhg-gmt-2.3.4 " +#configopts += "-DCOPY_DCW=TRUE -DDCW_ROOT=/tmp/hajgato/build/GMT/5.1.2/intel-2015a/dcw-gmt-1.1.1 " + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/gmt', 'bin/isogmt'], + 'dirs': [] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.2_netCDF.patch b/easybuild/easyconfigs/g/GMT/GMT-5.1.2_netCDF.patch new file mode 100644 index 0000000000..80cdf09d69 --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.2_netCDF.patch @@ -0,0 +1,23 @@ +#Do not check netCDF LD_LIBRARY_PATH dependencies using nc-config --libs, as we provide with EB +#B. Hajgato August 20th, 2015 +--- gmt-5.1.2/cmake/modules/FindNETCDF.cmake.old 2014-02-01 00:39:56.000000000 +0100 ++++ gmt-5.1.2/cmake/modules/FindNETCDF.cmake 2015-08-20 11:06:25.039494965 +0200 +@@ -106,12 +106,12 @@ + ) + + # find all libs that nc-config reports +-foreach (_extralib ${_netcdf_lib}) +- find_library (_found_lib_${_extralib} +- NAMES ${_extralib} +- PATHS ${_netcdf_libpath}) +- list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) +-endforeach (_extralib) ++#foreach (_extralib ${_netcdf_lib}) ++# find_library (_found_lib_${_extralib} ++# NAMES ${_extralib} ++# PATHS ${_netcdf_libpath}) ++# list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) ++#endforeach (_extralib) + + if (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + # Ensure that NetCDF with version 4 extensions is installed diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb new file mode 100644 index 0000000000..ed86b100ab --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -0,0 +1,32 @@ +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': '2015a'} +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')] + +builddependencies = [ + ('CMake', '3.2.2'), + ('Doxygen', '1.8.9.1', '', ('GCC', '4.9.2')), + ('cURL', '7.43.0'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' -- GitLab From fa91fe02ae8e8f5bc5e3d1b9cbb955e413700e50 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 24 Aug 2015 09:58:33 +0200 Subject: [PATCH 0907/1172] libxml2 moved form PR #1439 --- .../libxml2-2.9.2-intel-2015a-Python-2.7.9.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..59d56c4c28 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,27 @@ +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': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' -- GitLab From b2b95636dcbc126f8886d034f048989e7aa1990c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 12:43:27 +0100 Subject: [PATCH 0908/1172] New XQilla using Xerces 3.1.2 and fix long description --- ...Qilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb new file mode 100644 index 0000000000..70eea04166 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.0' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C∞ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +dependencies = [ + ('Xerces-C++', '3.1.2'), +] + +moduleclass = 'lib' -- GitLab From 670cef6ae979069d87fd740168c1689da42c2f2b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 15:52:46 +0100 Subject: [PATCH 0909/1172] Add XQilla versions for goolf and intel toolchains --- ...lla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb | 24 +++++++++++++++++++ ...illa-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb new file mode 100644 index 0000000000..b8e8a00615 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.0' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C∞ library.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +dependencies = [ + ('Xerces-C++', '3.1.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb new file mode 100644 index 0000000000..5421fe024f --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.0' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C∞ library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +dependencies = [ + ('Xerces-C++', '3.1.2'), +] + +moduleclass = 'lib' -- GitLab From 323d2592d14353ffc9bf88086912e84c7c7efd83 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 16:08:38 +0100 Subject: [PATCH 0910/1172] Use versionsuffix for Xerces dependency --- .../x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb | 5 ++++- .../x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb | 5 ++++- .../x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb index 70eea04166..625360f075 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb @@ -17,8 +17,11 @@ source_urls = [ configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' +xerces_version = '3.1.2' +versionsuffix = '-Xerces-C++-%s' % xerces_version + dependencies = [ - ('Xerces-C++', '3.1.2'), + ('Xerces-C++', '%s' % xerces_version ), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb index b8e8a00615..a1c35340eb 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb @@ -17,8 +17,11 @@ source_urls = [ configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' +xerces_version = '3.1.2' +versionsuffix = '-Xerces-C++-%s' % xerces_version + dependencies = [ - ('Xerces-C++', '3.1.2'), + ('Xerces-C++', '%s' % xerces_version ), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb index 5421fe024f..81cc5fc4cb 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb @@ -17,8 +17,11 @@ source_urls = [ configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' +xerces_version = '3.1.2' +versionsuffix = '-Xerces-C++-%s' % xerces_version + dependencies = [ - ('Xerces-C++', '3.1.2'), + ('Xerces-C++', '%s' % xerces_version ), ] moduleclass = 'lib' -- GitLab From 79c8213243a20a8b0ca802f6c0b849938b3c5548 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 16:25:56 +0100 Subject: [PATCH 0911/1172] Add Boost easyconfigs with Python 2.7.9 --- .../Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb | 27 +++++++++++++++++++ .../Boost-1.55.0-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb new file mode 100644 index 0000000000..349cfa6a3d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..856e218f9f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 0a71efda43124bb0d216697fb89bac407bc541a0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 16:27:55 +0100 Subject: [PATCH 0912/1172] Add Xerces 3.1.2 for goolf --- .../Xerces-C++-3.1.2-goolf-1.7.20.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..549b80498f --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/3/sources/' +] + +dependencies = [ + ('cURL', '7.44.0'), +] + +moduleclass = 'lib' -- GitLab From f03aa21f1bcd82ea8b8b27f5a47d0656aaad73ff Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 21:03:29 +0100 Subject: [PATCH 0913/1172] Use dynamic string for major release in URL --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb | 2 +- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb index 801f0ca105..e2bfd14b2a 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/3/sources/' + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb index 549b80498f..258f78b64a 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/3/sources/' + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb index c6c6bc70ec..78f997327e 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = ['xerces-c-%(version)s.tar.gz'] source_urls = [ - 'http://apache.belnet.be/xerces/c/3/sources/' + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' ] dependencies = [ -- GitLab From 542381714d71bebac7bc1ed35afa502db734544d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 21:09:08 +0100 Subject: [PATCH 0914/1172] Fix dynamic string for Xerces dependency --- .../x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb | 2 +- .../x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb | 2 +- .../x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb index 625360f075..8c56f4f186 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb @@ -21,7 +21,7 @@ xerces_version = '3.1.2' versionsuffix = '-Xerces-C++-%s' % xerces_version dependencies = [ - ('Xerces-C++', '%s' % xerces_version ), + ('Xerces-C++', xerces_version), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb index a1c35340eb..1f717f8250 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb @@ -21,7 +21,7 @@ xerces_version = '3.1.2' versionsuffix = '-Xerces-C++-%s' % xerces_version dependencies = [ - ('Xerces-C++', '%s' % xerces_version ), + ('Xerces-C++', xerces_version), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb index 81cc5fc4cb..6cb97c603d 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb @@ -21,7 +21,7 @@ xerces_version = '3.1.2' versionsuffix = '-Xerces-C++-%s' % xerces_version dependencies = [ - ('Xerces-C++', '%s' % xerces_version ), + ('Xerces-C++', xerces_version), ] moduleclass = 'lib' -- GitLab From d9859bb13013236c14cf0f1ac55b571e8bbdfba6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 21:18:58 +0100 Subject: [PATCH 0915/1172] Use Python 2.7.10 --- ...Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb | 27 +++++++++++++++++++ ...Qilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb | 2 +- ...lla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb | 2 +- ...illa-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb | 2 +- 4 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb new file mode 100644 index 0000000000..737090b731 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb index 8c56f4f186..a327ed16c6 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb index 1f717f8250..3b02d175c9 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb index 6cb97c603d..4119553446 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' -- GitLab From 746fde2c5343d31873534d65b8f3bf4eb90d887e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2015 21:59:24 +0100 Subject: [PATCH 0916/1172] Add Python 2.7.10 for goolf 1.7.20 --- .../p/Python/Python-2.7.10-goolf-1.7.20.eb | 122 ++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb new file mode 100644 index 0000000000..91fd31b728 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +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 = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' -- GitLab From 98252e66d9ed7884e5c7d62c9f512cdb53025980 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Aug 2015 09:43:14 +0200 Subject: [PATCH 0917/1172] {math}[intel/2015a] sympy 0.7.6 w/ Python 2.7.10 --- .../sympy-0.7.6-intel-2015a-Python-2.7.10.eb | 34 +++++++ .../sympy/sympy-0.7.6_fix-numpy-include.patch | 98 +++++++++++++++++++ 2 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..8932209250 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '0.7.6' + +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': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] +sources = [SOURCE_TAR_GZ] + +patches = ['sympy-%(version)s_fix-numpy-include.patch'] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [(python, pyver)] + +runtest = 'CPATH=$EBROOTPYTHON/lib/python%s/site-packages/numpy/core/include:$CPATH python setup.py test' % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sympy' % pyshortver], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch b/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch new file mode 100644 index 0000000000..6e2d922fad --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch @@ -0,0 +1,98 @@ +see https://github.com/sympy/sympy/pull/8848 + +From 1615390dff374f67fe12a13a424435e2725f3e79 Mon Sep 17 00:00:00 2001 +From: "Jason K. Moore" +Date: Mon, 19 Jan 2015 09:48:48 -0800 +Subject: [PATCH] Added np.get_include() to Cython autowrapper, fixes #8847. + +- Made CodeWrapper a new style class. +- Moved _need_numpy into __init__ so it doesn't pollute other instances. +- Optionally include numpy include directories in Cython setup.py. +--- + sympy/utilities/autowrap.py | 51 ++++++++++++++++++++++++++++----------------- + 1 file changed, 32 insertions(+), 19 deletions(-) + +diff --git a/sympy/utilities/autowrap.py b/sympy/utilities/autowrap.py +index bed39ef..8af7fbf 100644 +--- a/sympy/utilities/autowrap.py ++++ b/sympy/utilities/autowrap.py +@@ -93,7 +93,7 @@ class CodeWrapError(Exception): + pass + + +-class CodeWrapper: ++class CodeWrapper(object): + """Base Class for code wrappers""" + _filename = "wrapped_code" + _module_basename = "wrapper_module" +@@ -211,30 +211,35 @@ class CythonCodeWrapper(CodeWrapper): + """Wrapper that uses Cython""" + + setup_template = ( +- "from distutils.core import setup\n" +- "from distutils.extension import Extension\n" +- "from Cython.Distutils import build_ext\n" +- "\n" +- "setup(\n" +- " cmdclass = {{'build_ext': build_ext}},\n" +- " ext_modules = [Extension({ext_args}, extra_compile_args=['-std=c99'])]\n" +- " )") ++ "from distutils.core import setup\n" ++ "from distutils.extension import Extension\n" ++ "from Cython.Distutils import build_ext\n" ++ "{np_import}" ++ "\n" ++ "setup(\n" ++ " cmdclass = {{'build_ext': build_ext}},\n" ++ " ext_modules = [Extension({ext_args},\n" ++ " extra_compile_args=['-std=c99'])],\n" ++ "{np_includes}" ++ " )") + + pyx_imports = ( +- "import numpy as np\n" +- "cimport numpy as np\n\n") ++ "import numpy as np\n" ++ "cimport numpy as np\n\n") + + pyx_header = ( +- "cdef extern from '{header_file}.h':\n" +- " {prototype}\n\n") ++ "cdef extern from '{header_file}.h':\n" ++ " {prototype}\n\n") + + pyx_func = ( +- "def {name}_c({arg_string}):\n" +- "\n" +- "{declarations}" +- "{body}") ++ "def {name}_c({arg_string}):\n" ++ "\n" ++ "{declarations}" ++ "{body}") + +- _need_numpy = False ++ def __init__(self, *args, **kwargs): ++ super(CythonCodeWrapper, self).__init__(*args, **kwargs) ++ self._need_numpy = False + + @property + def command(self): +@@ -251,8 +256,16 @@ def _prepare_files(self, routine): + + # setup.py + ext_args = [repr(self.module_name), repr([pyxfilename, codefilename])] ++ if self._need_numpy: ++ np_import = 'import numpy as np\n' ++ np_includes = ' include_dirs = [np.get_include()],\n' ++ else: ++ np_import = '' ++ np_includes = '' + with open('setup.py', 'w') as f: +- f.write(self.setup_template.format(ext_args=", ".join(ext_args))) ++ f.write(self.setup_template.format(ext_args=", ".join(ext_args), ++ np_import=np_import, ++ np_includes=np_includes)) + + @classmethod + def _get_wrapped_function(cls, mod, name): -- GitLab From 7f0f1581cf4f8120a6ffa84c9e5b0feba760a408 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Aug 2015 10:36:19 +0200 Subject: [PATCH 0918/1172] remove $CPATH trickery --- .../s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb index 8932209250..ffcc2cbe6c 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = "-%s-%s" % (python, pyver) dependencies = [(python, pyver)] -runtest = 'CPATH=$EBROOTPYTHON/lib/python%s/site-packages/numpy/core/include:$CPATH python setup.py test' % pyshortver +runtest = 'python setup.py test' sanity_check_paths = { 'files': [], -- GitLab From 1f7e55263a0afdefd7afb4ec4bd470b14d32f10f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Aug 2015 11:02:24 +0200 Subject: [PATCH 0919/1172] typos and styles corrected --- .../g/GMT/GMT-5.1.0-goolf-1.4.10.eb | 6 ++--- .../g/GMT/GMT-5.1.2-intel-2015a.eb | 13 +++++---- ...libxml2-2.9.2-intel-2015a-Python-2.7.10.eb | 27 +++++++++++++++++++ .../n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 4 +-- 4 files changed, 38 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb index 8ac6f24179..4fc4997906 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb @@ -1,8 +1,8 @@ +easyblock = "CMakeMake" + name = "GMT" version = "5.1.0" -easyblock = "CMakeMake" - homepage = 'http://gmt.soest.hawaii.edu/' description = """GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, @@ -14,7 +14,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = ['gmt-%(version)s-src.tar.bz2'] # http download requires flash enabled browser -#http://gmt.soest.hawaii.edu/files/download?name= +# http://gmt.soest.hawaii.edu/files/download?name= source_urls = [ 'ftp://ftp.soest.hawaii.edu/gmt', 'ftp://ftp.soest.hawaii.edu/gmt/legacy', diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb index 8f2f3a4f84..d06010de6a 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb @@ -1,7 +1,8 @@ +easyblock = "CMakeMake" + name = "GMT" version = "5.1.2" -easyblock = "CMakeMake" homepage = 'http://gmt.soest.hawaii.edu/' description = """GMT is an open source collection of about 80 command-line tools for manipulating @@ -16,13 +17,13 @@ gshhg_ver = '2.3.4' dcw_ver = '1.1.1' sources = [ 'gmt-%(version)s-src.tar.bz2', - #coastlines, rivers, and political boundaries + # coastlines, rivers, and political boundaries 'gshhg-gmt-%s.tar.gz' % gshhg_ver, - #country polygons + # country polygons 'dcw-gmt-%s.tar.gz' % dcw_ver, ] -#'http://gmt.soest.hawaii.edu/files/download?name=' needs flash enabled browser +# 'http://gmt.soest.hawaii.edu/files/download?name=' needs flash enabled browser source_urls = [ 'ftp://ftp.soest.hawaii.edu/gmt', 'ftp://ftp.soest.hawaii.edu/gmt/legacy', @@ -32,7 +33,7 @@ source_urls = [ 'ftp://ftp.soest.hawaii.edu/dcw/legacy', ] -patches = ['GMT-5.1.2_netCDF.patch'] +patches = ['GMT-%(version)s_netCDF.patch'] builddependencies = [('CMake', '3.2.2')] @@ -46,8 +47,6 @@ dependencies = [ configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % gshhg_ver configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % dcw_ver -#configopts = "-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=/tmp/hajgato/build/GMT/5.1.2/intel-2015a/gshhg-gmt-2.3.4 " -#configopts += "-DCOPY_DCW=TRUE -DDCW_ROOT=/tmp/hajgato/build/GMT/5.1.2/intel-2015a/dcw-gmt-1.1.1 " separate_build_dir = True diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..da461a3caf --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,27 @@ +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': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index ed86b100ab..26fe030ea0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -25,8 +25,8 @@ builddependencies = [ # make sure both static and shared libs are built configopts = [ - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.a", ] moduleclass = 'data' -- GitLab From ee903abcc3b197127383baefa3158a87458d1c31 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 25 Aug 2015 11:13:50 +0100 Subject: [PATCH 0920/1172] Update XQilla to 2.3.2 and remove Xerces versionsuffix --- .../x/XQilla/XQilla-2.3.2-foss-2015a.eb | 26 +++++++++++++++++++ .../x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb | 26 +++++++++++++++++++ .../x/XQilla/XQilla-2.3.2-intel-2015a.eb | 26 +++++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb new file mode 100644 index 0000000000..f50e6f7c6f --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..f49deadfa8 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb new file mode 100644 index 0000000000..4465efd33d --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' -- GitLab From acff99c9695c409e8aee352f786feefa9ecda47e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 25 Aug 2015 14:24:00 +0100 Subject: [PATCH 0921/1172] Fix download URL for XQilla --- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb index f50e6f7c6f..b87a99e053 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', + 'http://downloads.sourceforge.net/project/xqilla/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb index f49deadfa8..9c1ac86436 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', + 'http://downloads.sourceforge.net/project/xqilla/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb index 4465efd33d..dd0f81fb20 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', + 'http://downloads.sourceforge.net/project/xqilla/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' -- GitLab From 78a1a6f8b75be92bc975e8ae5dcefe38b6b9a3ff Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 25 Aug 2015 14:55:20 +0100 Subject: [PATCH 0922/1172] Fix XQilla download URL properly --- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb index b87a99e053..d7fbf95394 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/', + 'http://downloads.sourceforge.net/project/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb index 9c1ac86436..c6db3af286 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/', + 'http://downloads.sourceforge.net/project/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb index dd0f81fb20..1fe033551c 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/', + 'http://downloads.sourceforge.net/project/xqilla/', ] configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' -- GitLab From 8d975329f77a7429f31be50be7ffe860635a729f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Aug 2015 16:16:32 +0200 Subject: [PATCH 0923/1172] version 2015a added --- easybuild/easyconfigs/m/MCR/MCR-R2015a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2015a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb new file mode 100644 index 0000000000..e0b5326bd6 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -0,0 +1,16 @@ +name = 'MCR' +version = 'R2015a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies =[('Java', '1.8.0_31')] + +moduleclass = 'math' -- GitLab From 8584d794fced1ed1a35b29d2fecd19bca9ce20fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Aug 2015 20:37:46 +0200 Subject: [PATCH 0924/1172] use patch to fix numpy include issues in all sympy 0.7.6 easyconfigs --- .../easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb index 4722866acf..7d47c242de 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] sources = [SOURCE_TAR_GZ] +patches = ['sympy-%(version)s_fix-numpy-include.patch'] + python = "Python" pythonversion = '2.7.9' pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) -- GitLab From 59e056e14e7ad29c6790e7e99d8aa6b6a92bb6d8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 25 Aug 2015 23:52:30 +0100 Subject: [PATCH 0925/1172] Fix Python version dep for goolf 1.7.20 --- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 91fd31b728..e5f6c7aacc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), - ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto + ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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 751e4a53a7a7b4d97236352d1f04570015c8c150 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 25 Aug 2015 23:54:12 +0100 Subject: [PATCH 0926/1172] Remove obsolete XQilla upgrades --- ...Qilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb | 27 ------------------- ...lla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb | 27 ------------------- ...illa-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb | 27 ------------------- 3 files changed, 81 deletions(-) delete mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb delete mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb delete mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb deleted file mode 100644 index a327ed16c6..0000000000 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a-Xerces-C++-3.1.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'XQilla' -version = '2.3.0' - -homepage = 'http://xqilla.sourceforge.net/HomePage' - -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C∞ library.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', -] - -configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' - -xerces_version = '3.1.2' -versionsuffix = '-Xerces-C++-%s' % xerces_version - -dependencies = [ - ('Xerces-C++', xerces_version), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb deleted file mode 100644 index 3b02d175c9..0000000000 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-goolf-1.7.20-Xerces-C++-3.1.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'XQilla' -version = '2.3.0' - -homepage = 'http://xqilla.sourceforge.net/HomePage' - -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C∞ library.""" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} - -sources = [SOURCE_TAR_GZ] -source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', -] - -configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' - -xerces_version = '3.1.2' -versionsuffix = '-Xerces-C++-%s' % xerces_version - -dependencies = [ - ('Xerces-C++', xerces_version), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb deleted file mode 100644 index 4119553446..0000000000 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a-Xerces-C++-3.1.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'XQilla' -version = '2.3.0' - -homepage = 'http://xqilla.sourceforge.net/HomePage' - -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C∞ library.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -sources = [SOURCE_TAR_GZ] -source_urls = [ - 'http://downloads.sourceforge.net/project/xqilla/xqilla/%(version)s', -] - -configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' - -xerces_version = '3.1.2' -versionsuffix = '-Xerces-C++-%s' % xerces_version - -dependencies = [ - ('Xerces-C++', xerces_version), -] - -moduleclass = 'lib' -- GitLab From 3a08b50318a7533c66fc73bba8fab5d3e8d310ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Aug 2015 10:24:09 +0200 Subject: [PATCH 0927/1172] {bio}[dummy] FoldX 3.0 beta 6.1 --- .../easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb | 21 +++++++++++++++++++ .../easyconfigs/f/FoldX/FoldX-3.0-beta6.eb | 1 + 2 files changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb new file mode 100644 index 0000000000..515869ebb7 --- /dev/null +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb @@ -0,0 +1,21 @@ +name = 'FoldX' +version = '3.0-beta6.1' + +homepage = 'http://foldx.crg.es/' +description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions + contributing to the stability of proteins and protein complexes.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URLs because registration is required to obtain sources +sources = ['%(name)s_30b6_linux64.zip'] +checksums = ['4b95ea518415d0d3be020f5f75c14e82'] + +start_dir = 'FoldX_30b6_linux64' + +sanity_check_paths = { + 'files': ["bin/foldx3b6", "rotabase.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb index 7585ccc7fc..adf1facd29 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb @@ -9,6 +9,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # no source URLs because registration is required to obtain sources sources = ['%(name)s_30b6_linux64.zip'] +checksums = ['d3264460a4fe08b57553ebcdaad2dcad'] sanity_check_paths = { 'files': ["bin/%(namelower)s64Linux", "rotabase.txt"], -- GitLab From 40db58b9f8814008d14e90bde0f0f311a96649a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Aug 2015 10:32:13 +0200 Subject: [PATCH 0928/1172] fix remark --- easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb | 1 + easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb index 515869ebb7..264a1ea82d 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb @@ -8,6 +8,7 @@ description = """FoldX is used to provide a fast and quantitative estimation of toolchain = {'name': 'dummy', 'version': 'dummy'} # no source URLs because registration is required to obtain sources +# same name as zip file for 3.0 beta 6 >_< sources = ['%(name)s_30b6_linux64.zip'] checksums = ['4b95ea518415d0d3be020f5f75c14e82'] diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb index adf1facd29..4eedd88eaa 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb @@ -8,6 +8,7 @@ description = """FoldX is used to provide a fast and quantitative estimation of toolchain = {'name': 'dummy', 'version': 'dummy'} # no source URLs because registration is required to obtain sources +# same name as zip file for 3.0 beta 6.1 >_< sources = ['%(name)s_30b6_linux64.zip'] checksums = ['d3264460a4fe08b57553ebcdaad2dcad'] -- GitLab From 258fdafa8e113b0a7457cb805a1fff5a1ab2e59c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 26 Aug 2015 10:18:47 +0100 Subject: [PATCH 0929/1172] SQLite and GMP deps. for goolf-1.7.20 --- .../g/GMP/GMP-6.0.0a-goolf-1.7.20.eb | 25 ++++++++++++ .../s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb | 40 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb new file mode 100644 index 0000000000..2eb33b2441 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +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' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..3ad3a9145a --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-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 = '3.8.10.2' + +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' + ''.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.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From e5107faf10ee32f4e9298e64da3ef4419106be6e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 26 Aug 2015 10:35:53 +0100 Subject: [PATCH 0930/1172] Add GMP 6 with GCC 4.8.4, as req. by goolf-1.7.20 --- ...GMP-6.0.0a-goolf-1.7.20.eb => GMP-6.0.0a-GCC-4.8.4.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GMP/{GMP-6.0.0a-goolf-1.7.20.eb => GMP-6.0.0a-GCC-4.8.4.eb} (67%) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb similarity index 67% rename from easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb rename to easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb index 2eb33b2441..86bd52156f 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.8.4.eb @@ -7,10 +7,10 @@ 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'} +toolchain = {'name': 'GCC', 'version': '4.8.4'} -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] # enable C++ interface configopts = '--enable-cxx' @@ -18,7 +18,7 @@ configopts = '--enable-cxx' runtest = 'check' sanity_check_paths = { - 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'files': ['lib/libgmp.so', 'include/gmp.h'], 'dirs': [], } -- GitLab From 5de575bb1ce968344f27b1f337baa5ef6ec5958d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Aug 2015 11:50:55 +0200 Subject: [PATCH 0931/1172] extend list of Bioconductor packages with derfinder/polyester --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 4 ++++ .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index db382cbce8..f4e89df8a7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -128,6 +128,10 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), + ('GenomicFiles', '1.4.0', bioconductor_options), + ('derfinderHelper', '1.2.0', bioconductor_options), + ('derfinder', '1.2.1', bioconductor_options), + ('polyester', '1.4.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index dd15792423..2c428f8a32 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -128,6 +128,10 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), + ('GenomicFiles', '1.4.0', bioconductor_options), + ('derfinderHelper', '1.2.0', bioconductor_options), + ('derfinder', '1.2.1', bioconductor_options), + ('polyester', '1.4.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} -- GitLab From 27863327cf62f9ff9091aece911d622de8cbb460 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Aug 2015 15:01:55 +0200 Subject: [PATCH 0932/1172] add easyconfig file for MATLAB 2015a --- .../easyconfigs/m/MATLAB/MATLAB-2015a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb new file mode 100644 index 0000000000..acdae43db5 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -0,0 +1,20 @@ +name = 'MATLAB' +version = '2015a' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_45')] + +import os +license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') +license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') +key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') + +moduleclass = 'math' -- GitLab From 3c1652b9cea292c74658d0546452ac0464842681 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 26 Aug 2015 15:28:51 +0200 Subject: [PATCH 0933/1172] netCDF tweaked --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 26fe030ea0..24e6aec104 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -24,9 +24,10 @@ builddependencies = [ ] # make sure both static and shared libs are built +common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include " configopts = [ - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so", - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.a", + common_configopts + "-DBUILD_SHARED_LIBS=ON -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so", + common_configopts + "-DBUILD_SHARED_LIBS=OFF -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.a", ] moduleclass = 'data' -- GitLab From 24f989e7fe3fca1a4c356462d3017c183558a62c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 26 Aug 2015 15:41:17 +0100 Subject: [PATCH 0934/1172] Remove obsolete config option for Boost --- .../b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb index 737090b731..5118cf95ff 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', pythonversion), ] -configopts = '--without-libraries=python' +#configopts = '--without-libraries=python' # also build boost_mpi boost_mpi = True -- GitLab From 94b92e134ac2b00578f7e254cdd7e7059eefb99f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 09:16:34 +0200 Subject: [PATCH 0935/1172] use static curl --- .../easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 24e6aec104..23d586e141 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -24,10 +24,11 @@ builddependencies = [ ] # make sure both static and shared libs are built -common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include " +common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.{0} -DCURL_INCLUDE_DIR=$EBROOTCURL/include " +common_configopts += "-DBUILD_SHARED_LIBS={1} -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.{0} " configopts = [ - common_configopts + "-DBUILD_SHARED_LIBS=ON -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so", - common_configopts + "-DBUILD_SHARED_LIBS=OFF -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.a", + common_configopts.format('so', 'ON'}, + common_configopts.format('a', 'OFF'}, ] moduleclass = 'data' -- GitLab From 346742058d10b1610f63e2a77bd46b32567bdb48 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 09:28:55 +0200 Subject: [PATCH 0936/1172] build static libs first --- .../easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 23d586e141..142f3ebca6 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -24,11 +24,11 @@ builddependencies = [ ] # make sure both static and shared libs are built -common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.{0} -DCURL_INCLUDE_DIR=$EBROOTCURL/include " -common_configopts += "-DBUILD_SHARED_LIBS={1} -DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.{0} " +configopts_tmpl = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.{0} -DCURL_INCLUDE_DIR=$EBROOTCURL/include " +configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.{0} -DBUILD_SHARED_LIBS={1} " configopts = [ - common_configopts.format('so', 'ON'}, - common_configopts.format('a', 'OFF'}, + configopts_tmpl.format('a', 'OFF'}, + configopts_tmpl.format('so', 'ON'}, ] moduleclass = 'data' -- GitLab From 077a4126d61419e187b55fd65016c638f0ccfe16 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 09:46:30 +0200 Subject: [PATCH 0937/1172] typo corrected --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 142f3ebca6..9b3a240499 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -27,8 +27,8 @@ builddependencies = [ configopts_tmpl = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.{0} -DCURL_INCLUDE_DIR=$EBROOTCURL/include " configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.{0} -DBUILD_SHARED_LIBS={1} " configopts = [ - configopts_tmpl.format('a', 'OFF'}, - configopts_tmpl.format('so', 'ON'}, + configopts_tmpl.format('a', 'OFF'), + configopts_tmpl.format('so', 'ON'), ] moduleclass = 'data' -- GitLab From 53be61cafdb82eac8f535b38d3bbfdb5a5e79821 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 12:13:30 +0200 Subject: [PATCH 0938/1172] Explicitly defined linking libs --- .../n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 9b3a240499..88511418f8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -15,20 +15,26 @@ source_urls = [ 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', ] -dependencies = [('HDF5', '1.8.15')] +dependencies = [ + ('HDF5', '1.8.15'), + ('cURL', '7.43.0'), +] builddependencies = [ ('CMake', '3.2.2'), ('Doxygen', '1.8.9.1', '', ('GCC', '4.9.2')), - ('cURL', '7.43.0'), ] # make sure both static and shared libs are built -configopts_tmpl = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.{0} -DCURL_INCLUDE_DIR=$EBROOTCURL/include " -configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.{0} -DBUILD_SHARED_LIBS={1} " +configopts_tmpl = '-DBUILD_SHARED_LIBS={0} -DCMAKE_C_FLAGS_DEBUG="" ' +configopts_tmpl += "-DHDF5_LIB=$EBROOTHDF5/lib/libhdf5.so -DHDF5_HL_LIB=$EBROOTHDF5/lib/libhdf5_hl.so " +configopts_tmpl += "-DHDF5_INCLUDE_DIR=$EBROOTHDF5/include " +configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so " +configopts_tmpl += "-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so " +configopts_tmpl += "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include " configopts = [ - configopts_tmpl.format('a', 'OFF'), - configopts_tmpl.format('so', 'ON'), + configopts_tmpl.format('OFF'), + configopts_tmpl.format('ON'), ] moduleclass = 'data' -- GitLab From f53c7375b3cb44cc6620e8380497eed38cc8b1bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 12:28:20 +0200 Subject: [PATCH 0939/1172] style fixes in tbb easyconfig + rename 4.0.x specific patch --- easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 8 ++++---- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 8 ++++---- .../{tbb_productsdb.patch => tbb-4.0_productsdb.patch} | 0 easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/t/tbb/{tbb_productsdb.patch => tbb-4.0_productsdb.patch} (100%) diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index b371961dbf..a157686a4a 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -13,14 +13,14 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_%s_%s.tgz' % (name, version)] +sources = ['l_%(name)s_%(version)s.tgz'] -patches = ['tbb_productsdb.patch'] - -moduleclass = 'lib' +patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index f5ecd2fd39..150aaf30f9 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -13,14 +13,14 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_%s_%s.tgz' % (name, version)] +sources = ['l_%(name)s_%(version)s.tgz'] -patches = ['tbb_productsdb.patch'] - -moduleclass = 'lib' +patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb_productsdb.patch b/easybuild/easyconfigs/t/tbb/tbb-4.0_productsdb.patch similarity index 100% rename from easybuild/easyconfigs/t/tbb/tbb_productsdb.patch rename to easybuild/easyconfigs/t/tbb/tbb-4.0_productsdb.patch diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index 8b1426bc88..27609d139f 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -13,12 +13,12 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_%s_%s.tgz' % (name, version)] - -moduleclass = 'lib' +sources = ['l_%(name)s_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' -- GitLab From be77152cbecff4b870c0c367f25a61a39d99e975 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 12:29:22 +0200 Subject: [PATCH 0940/1172] build type set to release --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 88511418f8..a0191bd9cd 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -26,7 +26,7 @@ builddependencies = [ ] # make sure both static and shared libs are built -configopts_tmpl = '-DBUILD_SHARED_LIBS={0} -DCMAKE_C_FLAGS_DEBUG="" ' +configopts_tmpl = "-DBUILD_SHARED_LIBS={0} -DCMAKE_BUILD_TYPE=RELEASE " configopts_tmpl += "-DHDF5_LIB=$EBROOTHDF5/lib/libhdf5.so -DHDF5_HL_LIB=$EBROOTHDF5/lib/libhdf5_hl.so " configopts_tmpl += "-DHDF5_INCLUDE_DIR=$EBROOTHDF5/include " configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so " -- GitLab From e7be83ecb731e81b3a3f4f4b5beb61b730dfddfc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 27 Aug 2015 13:54:22 +0200 Subject: [PATCH 0941/1172] c_flag_release added --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index a0191bd9cd..19de9ccda0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -26,7 +26,7 @@ builddependencies = [ ] # make sure both static and shared libs are built -configopts_tmpl = "-DBUILD_SHARED_LIBS={0} -DCMAKE_BUILD_TYPE=RELEASE " +configopts_tmpl = '-DBUILD_SHARED_LIBS={0} -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG " ' configopts_tmpl += "-DHDF5_LIB=$EBROOTHDF5/lib/libhdf5.so -DHDF5_HL_LIB=$EBROOTHDF5/lib/libhdf5_hl.so " configopts_tmpl += "-DHDF5_INCLUDE_DIR=$EBROOTHDF5/include " configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so " -- GitLab From 729192d9d71721b962e7b277ad1ba432f749ea39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 15:13:08 +0200 Subject: [PATCH 0942/1172] {cae}[*/2015b] OpenFOAM 2.3.1 + deps --- .../f/flex/flex-2.5.39-foss-2015b.eb | 14 ++++++++ .../f/flex/flex-2.5.39-intel-2015b.eb | 14 ++++++++ .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb | 32 +++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb | 32 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb | 14 ++++++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb | 14 ++++++++ 6 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb new file mode 100644 index 0000000000..40befb9e4a --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb new file mode 100644 index 0000000000..159eef3274 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.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': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb new file mode 100644 index 0000000000..24739eaae8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb @@ -0,0 +1,32 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +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': 'foss', 'version': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb new file mode 100644 index 0000000000..3c1706af3a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb @@ -0,0 +1,32 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +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': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb new file mode 100644 index 0000000000..3f65d37408 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb new file mode 100644 index 0000000000..34df491afd --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.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': '2015b'} +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 b77f0b05877f0e0e1b575fc63c945baf6bbc4cdf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 20:27:32 +0200 Subject: [PATCH 0943/1172] {lib}[*/2015a] NFFT 3.3.0 --- .../n/NFFT/NFFT-3.3.0-foss-2015a.eb | 23 +++++++++++++++++++ .../n/NFFT/NFFT-3.3.0-intel-2015a.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb new file mode 100644 index 0000000000..263c3c6dac --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('FFTW', '3.3.4', '', ('gompi', '2015a'))] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb new file mode 100644 index 0000000000..0e939b4038 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('FFTW', '3.3.4')] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 95257976961145eaaed52a28bd475f601bfef418 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 22:19:42 +0200 Subject: [PATCH 0944/1172] bump to R v3.2.1 --- .../c/cURL/cURL-7.43.0-intel-2015b.eb | 31 ++ ....eb => libjpeg-turbo-1.4.1-intel-2015b.eb} | 4 +- .../l/libpng/libpng-1.6.16-intel-2015b.eb | 19 -- ...l-2015b.eb => NASM-2.11.08-intel-2015b.eb} | 2 +- .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb | 21 ++ ...5b-bare.eb => R-3.2.1-intel-2015b-bare.eb} | 4 +- ...-intel-2015b.eb => R-3.2.1-intel-2015b.eb} | 306 ++++++++---------- 7 files changed, 199 insertions(+), 188 deletions(-) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb rename easybuild/easyconfigs/l/libjpeg-turbo/{libjpeg-turbo-1.4.0-intel-2015b.eb => libjpeg-turbo-1.4.1-intel-2015b.eb} (93%) delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb rename easybuild/easyconfigs/n/NASM/{NASM-2.11.06-intel-2015b.eb => NASM-2.11.08-intel-2015b.eb} (97%) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb rename easybuild/easyconfigs/r/R/{R-3.2.0-intel-2015b-bare.eb => R-3.2.1-intel-2015b-bare.eb} (91%) rename easybuild/easyconfigs/r/R/{R-3.1.3-intel-2015b.eb => R-3.2.1-intel-2015b.eb} (57%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb new file mode 100644 index 0000000000..853014d95e --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': '2015b'} + +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.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb similarity index 93% rename from easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb rename to easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb index 2bb0e8f9bc..49b99b98b3 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libjpeg-turbo' -version = '1.4.0' +version = '1.4.1' 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 @@ -15,7 +15,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('NASM', '2.11.06'), + ('NASM', '2.11.08'), ] configopts = "--with-jpeg8" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb deleted file mode 100644 index 21ff2f7764..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -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': 'intel', 'version': '2015b'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb similarity index 97% rename from easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb rename to easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb index f174be96fd..92d511ac9c 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'NASM' -version = '2.11.06' +version = '2.11.08' homepage = 'http://www.nasm.us/' description = """NASM: General-purpose x86 assembler""" 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 new file mode 100644 index 0000000000..a34f9121d1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': 'intel', 'version': '2015b'} +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'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb similarity index 91% rename from easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb rename to easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb index f840c8adba..3fb6481118 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb @@ -1,5 +1,5 @@ name = 'R' -version = '3.2.0' +version = '3.2.1' versionsuffix = '-bare' homepage = 'http://www.r-project.org/' @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R - ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb similarity index 57% rename from easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb rename to easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb index e1e96bff04..f9b3e10876 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb @@ -1,5 +1,5 @@ name = 'R' -version = '3.1.3' +version = '3.2.1' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,11 +17,13 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R - ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -33,18 +35,7 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} + # !! order of packages is important !! # packages updated on January 8th 2015 @@ -69,199 +60,198 @@ exts_list = [ ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), - ('bnlearn', '3.7.1', ext_options), + ('bnlearn', '3.8.1', ext_options), ('bootstrap', '2015.2', ext_options), ('combinat', '0.0-8', ext_options), ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), + ('highr', '0.5', ext_options), ('infotheo', '1.2.0', ext_options), ('lars', '1.2', ext_options), ('lazy', '1.2-15', ext_options), ('kernlab', '0.9-20', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-6', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), ('rmeta', '2.16', ext_options), ('segmented', '0.5-1.1', ext_options), ('som', '0.3-5', ext_options), ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), + ('stabledist', '0.7-0', ext_options), ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), + ('pspline', '1.0-17', ext_options), ('timeDate', '3012.100', ext_options), ('longmemo', '1.0-0', ext_options), ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), + ('ade4', '1.7-2', ext_options), ('AlgDesign', '1.1-7.3', ext_options), ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), + ('BH', '1.58.0-1', ext_options), ('brew', '1.0-6', ext_options), ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.11', ext_options), - ('checkmate', '1.5.2', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), ('cubature', '1.1-2', ext_options), ('DEoptimR', '1.0-2', ext_options), ('digest', '0.6.8', ext_options), ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), + ('ffbase', '0.12.1', ext_options), ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), + ('maps', '2.3-10', ext_options), ('nnls', '1.4', ext_options), ('sendmailR', '1.2-1', ext_options), ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.5.5', ext_options), - ('logspline', '2.1.5', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-11', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), ('randomForest', '4.6-10', ext_options), ('scatterplot3d', '0.3-35', ext_options), ('SparseM', '1.6', ext_options), ('tripack', '1.3-6', ext_options), ('irace', '1.06', ext_options), ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-30', ext_options), + ('lattice', '0.20-31', ext_options), ('RColorBrewer', '1.1-2', ext_options), ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-5', ext_options), + ('Matrix', '1.2-2', ext_options), ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), ('quadprog', '1.5-5', ext_options), ('BB', '2014.10-1', ext_options), ('BBmisc', '1.9', ext_options), ('fail', '1.2', ext_options), ('rlecuyer', '0.3-3', ext_options), ('snow', '0.3-13', ext_options), - ('MASS', '7.3-40', ext_options), - ('tree', '1.0-35', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), ('pls', '2.4-3', ext_options), - ('class', '7.3-12', ext_options), + ('class', '7.3-13', ext_options), ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-9', ext_options), - ('nlme', '3.1-120', ext_options), - ('mgcv', '1.8-5', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), ('minqa', '1.2.4', ext_options), - ('nloptr', '1.0.4', ext_options), ('RcppEigen', '0.3.2.4.0', ext_options), - ('lme4', '1.1-7', ext_options), - ('pbkrtest', '0.4-2', ext_options), ('quantreg', '5.11', ext_options), - ('car', '2.0-25', ext_options), + ('mgcv', '1.8-6', ext_options), ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-9', ext_options), + ('rpart', '4.1-10', ext_options), ('mice', '2.22', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), ('logistf', '1.21', ext_options), ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), - ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '2.0.1', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), ('gclus', '1.3.1', ext_options), ('coda', '0.17-1', ext_options), ('codetools', '0.2-11', ext_options), ('foreach', '1.4.2', ext_options), ('doMC', '1.3.3', ext_options), ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-63', ext_options), - ('survival', '2.38-1', ext_options), - ('gam', '1.09.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), ('gamlss.data', '4.2-7', ext_options), ('gamlss.dist', '4.3-4', ext_options), ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-14', ext_options), - ('zoo', '1.7-12', ext_options), + ('KernSmooth', '2.23-15', ext_options), ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), + ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), + ('mnormt', '1.5-3', ext_options), ('mvtnorm', '1.0-2', ext_options), ('pcaPP', 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ext_options), ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), + ('R.utils', '2.1.0', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.12.1', bioconductor_options), - ('Biobase', '2.26.0', bioconductor_options), - ('S4Vectors', '0.4.0', bioconductor_options), - ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.5', bioconductor_options), - ('AnnotationDbi', '1.28.2', bioconductor_options), - ('XVector', '0.6.0', bioconductor_options), - ('zlibbioc', '1.12.0', bioconductor_options), - ('Biostrings', '2.34.1', bioconductor_options), - ('GenomicRanges', '1.18.4', bioconductor_options), - ('Rsamtools', '1.18.3', bioconductor_options), - ('BiocParallel', '1.0.3', bioconductor_options), - ('GenomicAlignments', '1.2.2', bioconductor_options), - ('ShortRead', '1.24.0', bioconductor_options), - ('graph', '1.44.1', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-0', ext_options), + ('Formula', '1.2-1', ext_options), ('acepack', '1.3-3.3', ext_options), - ('gtable', '0.1.2', ext_options), ('reshape2', '1.4.1', ext_options), - ('proto', '0.3-10', ext_options), + ('gtable', '0.1.2', ext_options), ('munsell', '0.4.2', ext_options), ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), + ('scales', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), - ('Hmisc', '3.15-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('Hmisc', '3.16-0', ext_options), ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-45', ext_options), + ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), - ('igraph', '0.7.1', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), + ('igraph', '1.0.1', ext_options), ('GeneNet', '1.2.12', ext_options), - ('ape', '3.2', ext_options), + ('ape', '3.3', ext_options), ('htmltools', '0.2.6', ext_options), ('RJSONIO', '1.3-0', ext_options), ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.11.1', ext_options), - ('adegenet', '1.4-2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), ('adephylo', '1.1-6', ext_options), ('animation', '2.3', ext_options), @@ -269,7 +259,7 @@ exts_list = [ ('bigmemory', '4.4.6', ext_options), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.3-33', ext_options), + ('raster', '2.4-15', ext_options), ('dismo', '1.0-12', ext_options), ('expm', '0.99-1.1', ext_options), ('extrafontdb', '1.0', ext_options), @@ -279,8 +269,9 @@ exts_list = [ ('shapefiles', '0.7', ext_options), ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), + ('labdsv', '1.7-0', ext_options), ('MatrixModels', '0.4-0', ext_options), ('stabs', '0.5-1', ext_options), ('mboost', '2.4-2', ext_options), @@ -288,21 +279,22 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.9', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), ('TH.data', '1.0-6', ext_options), ('multcomp', '1.4-0', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('rms', '4.3-0', ext_options), + ('rms', '4.3-1', ext_options), ('RWekajars', '3.7.12-1', ext_options), ('RWeka', '0.4-24', ext_options), ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), + ('tm', '0.6-2', ext_options), ('TraMineR', '1.8-9', ext_options), ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), - ('statmod', '1.4.20', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), ('maxLik', '1.2-4', ext_options), ('mlogit', '0.2-4', ext_options), @@ -312,80 +304,66 @@ exts_list = [ ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), - ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.5', bioconductor_options), - ('preprocessCore', '1.28.0', bioconductor_options), - ('affy', '1.44.0', bioconductor_options), - ('GO.db', '3.0.0', bioconductor_options), - ('limma', '3.22.7', bioconductor_options), - ('RBGL', '1.42.0', bioconductor_options), - ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.2', bioconductor_options), - ('KEGG.db', '3.0.0', bioconductor_options), - ('annaffy', '1.38.0', bioconductor_options), - ('gcrma', '2.38.0', bioconductor_options), - ('oligoClasses', '1.28.0', bioconductor_options), - ('edgeR', '3.8.6', bioconductor_options), - ('PFAM.db', '3.0.0', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('GGally', '0.5.0', ext_options), - ('baySeq', '2.0.50', bioconductor_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), - ('qvalue', '1.43.0', bioconductor_options), - ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.14.0', ext_options), - ('samr', '2.0', ext_options), - ('DEGseq', '1.20.0', bioconductor_options), + ('matrixStats', '0.14.2', ext_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.29', ext_options), + ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), ('flexmix', '2.3-13', ext_options), ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), + ('diptest', '0.75-7', ext_options), ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.0.0', bioconductor_options), ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), - ('bumphunter', '1.6.0', bioconductor_options), - ('multtest', '2.22.0', bioconductor_options), - ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.6', ext_options), - ('DynDoc', '1.44.0', bioconductor_options), - ('genoset', '1.20.0', bioconductor_options), + ('nleqslv', '2.8', ext_options), ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.2', ext_options), - ('multtest', '2.22.0', bioconductor_options), - ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.4.0', ext_options), - ('Rgraphviz', '2.10.0', bioconductor_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), - ('RNASeqPower', '1.6.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('Rsubread', '1.16.1', bioconductor_options), - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk - ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('vegan', '2.3-0', ext_options), ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), ] moduleclass = 'lang' -- GitLab From 501356ef57fdba9f22718cbdebcf7d0113d32451 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 22:31:47 +0200 Subject: [PATCH 0945/1172] bump to R v3.2.1 --- .../c/cURL/cURL-7.43.0-foss-2015b.eb | 31 ++ ...b.eb => libjpeg-turbo-1.4.1-foss-2015b.eb} | 4 +- .../l/libxml2/libxml2-2.9.2-foss-2015b.eb | 28 ++ ...ss-2015b.eb => NASM-2.11.08-foss-2015b.eb} | 2 +- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb | 21 ++ ...15b-bare.eb => R-3.2.1-foss-2015b-bare.eb} | 4 +- ....3-foss-2015b.eb => R-3.2.1-foss-2015b.eb} | 309 ++++++++---------- 7 files changed, 228 insertions(+), 171 deletions(-) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb rename easybuild/easyconfigs/l/libjpeg-turbo/{libjpeg-turbo-1.4.0-foss-2015b.eb => libjpeg-turbo-1.4.1-foss-2015b.eb} (92%) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb rename easybuild/easyconfigs/n/NASM/{NASM-2.11.06-foss-2015b.eb => NASM-2.11.08-foss-2015b.eb} (97%) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb rename easybuild/easyconfigs/r/R/{R-3.2.0-foss-2015b-bare.eb => R-3.2.1-foss-2015b-bare.eb} (91%) rename easybuild/easyconfigs/r/R/{R-3.1.3-foss-2015b.eb => R-3.2.1-foss-2015b.eb} (56%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb new file mode 100644 index 0000000000..00dbb79c54 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': 'foss', 'version': '2015b'} + +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.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb similarity index 92% rename from easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb rename to easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb index d0e4377e82..eb2697c94d 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libjpeg-turbo' -version = '1.4.0' +version = '1.4.1' homepage = 'http://sourceforge.net/libjpeg-turbo/' description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG @@ -15,7 +15,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('NASM', '2.11.06'), + ('NASM', '2.11.08'), ] configopts = "--with-jpeg8" diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb new file mode 100644 index 0000000000..1c90dac8b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -0,0 +1,28 @@ +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': 'foss', 'version': '2015b'} + +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')] + +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/n/NASM/NASM-2.11.06-foss-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb similarity index 97% rename from easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015b.eb rename to easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb index 397b3d64f4..bcb04e7841 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'NASM' -version = '2.11.06' +version = '2.11.08' homepage = 'http://www.nasm.us/' description = """NASM: General-purpose x86 assembler""" 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 new file mode 100644 index 0000000000..080b203770 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': '2015b'} +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'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb similarity index 91% rename from easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb rename to easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb index 9c7b469262..c7ffa781a4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb @@ -1,5 +1,5 @@ name = 'R' -version = '3.2.0' +version = '3.2.1' versionsuffix = '-bare' homepage = 'http://www.r-project.org/' @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R - ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb similarity index 56% rename from easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb rename to easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb index 70a801b84e..1528a48e4d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -1,5 +1,5 @@ name = 'R' -version = '3.1.3' +version = '3.2.1' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,11 +17,13 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R - ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -33,18 +35,7 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} + # !! order of packages is important !! # packages updated on January 8th 2015 @@ -69,199 +60,198 @@ exts_list = [ ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), - ('bnlearn', '3.7.1', ext_options), + ('bnlearn', '3.8.1', ext_options), ('bootstrap', '2015.2', ext_options), ('combinat', '0.0-8', ext_options), ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), + ('highr', '0.5', ext_options), ('infotheo', '1.2.0', ext_options), ('lars', '1.2', ext_options), ('lazy', '1.2-15', ext_options), ('kernlab', '0.9-20', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-6', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), ('rmeta', '2.16', ext_options), ('segmented', '0.5-1.1', ext_options), ('som', '0.3-5', ext_options), ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), + ('stabledist', '0.7-0', ext_options), ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), + ('pspline', '1.0-17', ext_options), ('timeDate', '3012.100', ext_options), ('longmemo', '1.0-0', ext_options), ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), + ('ade4', '1.7-2', 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ext_options), - ('logspline', '2.1.5', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-11', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), ('randomForest', '4.6-10', ext_options), ('scatterplot3d', '0.3-35', ext_options), ('SparseM', '1.6', ext_options), ('tripack', '1.3-6', ext_options), ('irace', '1.06', ext_options), ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-30', ext_options), + ('lattice', '0.20-31', ext_options), ('RColorBrewer', '1.1-2', ext_options), ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-5', ext_options), + ('Matrix', '1.2-2', ext_options), ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), ('quadprog', '1.5-5', ext_options), ('BB', '2014.10-1', ext_options), ('BBmisc', '1.9', ext_options), ('fail', '1.2', ext_options), ('rlecuyer', '0.3-3', ext_options), ('snow', '0.3-13', ext_options), - ('MASS', '7.3-40', ext_options), - ('tree', '1.0-35', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), ('pls', '2.4-3', ext_options), - ('class', '7.3-12', ext_options), + ('class', '7.3-13', ext_options), ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-9', ext_options), - ('nlme', '3.1-120', ext_options), - ('mgcv', '1.8-5', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), ('minqa', '1.2.4', ext_options), - ('nloptr', '1.0.4', ext_options), ('RcppEigen', '0.3.2.4.0', ext_options), - ('lme4', '1.1-7', ext_options), - ('pbkrtest', '0.4-2', ext_options), ('quantreg', '5.11', ext_options), - ('car', '2.0-25', ext_options), + ('mgcv', '1.8-6', ext_options), ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-9', ext_options), + ('rpart', '4.1-10', ext_options), ('mice', '2.22', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), ('logistf', '1.21', ext_options), ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), - ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '2.0.1', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), ('gclus', '1.3.1', ext_options), ('coda', '0.17-1', ext_options), ('codetools', '0.2-11', ext_options), ('foreach', '1.4.2', ext_options), ('doMC', '1.3.3', ext_options), ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-63', ext_options), - ('survival', '2.38-1', ext_options), - ('gam', '1.09.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), ('gamlss.data', '4.2-7', ext_options), ('gamlss.dist', '4.3-4', ext_options), ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-14', ext_options), - ('zoo', '1.7-12', ext_options), + ('KernSmooth', '2.23-15', ext_options), ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), + ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), + ('mnormt', '1.5-3', ext_options), ('mvtnorm', '1.0-2', ext_options), ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.4.0', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.8', ext_options), + ('pscl', '1.4.9', ext_options), ('RSQLite', '1.0.0', ext_options), ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-2', ext_options), + ('sandwich', '2.3-3', ext_options), ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-9', ext_options), - ('VGAM', '0.9-7', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), ('waveslim', '1.7.5', ext_options), ('xtable', '1.7-4', ext_options), ('profileModel', '0.5-9', ext_options), ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), + ('deSolve', '1.12', ext_options), ('tseriesChaos', '0.1-13', ext_options), ('tseries', '0.10-34', ext_options), ('fastICA', '1.2-0', ext_options), ('R.methodsS3', '1.7.0', ext_options), ('R.oo', '1.19.0', ext_options), ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), + ('R.utils', '2.1.0', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.12.1', bioconductor_options), - ('Biobase', '2.26.0', bioconductor_options), - ('S4Vectors', '0.4.0', bioconductor_options), - ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.5', bioconductor_options), - ('AnnotationDbi', '1.28.2', bioconductor_options), - ('XVector', '0.6.0', bioconductor_options), - ('zlibbioc', '1.12.0', bioconductor_options), - ('Biostrings', '2.34.1', bioconductor_options), - ('GenomicRanges', '1.18.4', bioconductor_options), - ('Rsamtools', '1.18.3', bioconductor_options), - ('BiocParallel', '1.0.3', bioconductor_options), - ('GenomicAlignments', '1.2.2', bioconductor_options), - ('ShortRead', '1.24.0', bioconductor_options), - ('graph', '1.44.1', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-0', ext_options), + ('Formula', '1.2-1', ext_options), ('acepack', '1.3-3.3', ext_options), - ('gtable', '0.1.2', ext_options), ('reshape2', '1.4.1', ext_options), - ('proto', '0.3-10', ext_options), + ('gtable', '0.1.2', ext_options), ('munsell', '0.4.2', ext_options), ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), + ('scales', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), - ('Hmisc', '3.15-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('Hmisc', '3.16-0', ext_options), ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-45', ext_options), + ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), - ('igraph', '0.7.1', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), + ('igraph', '1.0.1', ext_options), ('GeneNet', '1.2.12', ext_options), - ('ape', '3.2', ext_options), + ('ape', '3.3', ext_options), ('htmltools', '0.2.6', ext_options), ('RJSONIO', '1.3-0', ext_options), ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.11.1', ext_options), - ('adegenet', '1.4-2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), ('adephylo', '1.1-6', ext_options), ('animation', '2.3', ext_options), @@ -269,7 +259,7 @@ exts_list = [ ('bigmemory', '4.4.6', ext_options), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.3-33', ext_options), + ('raster', '2.4-15', ext_options), ('dismo', '1.0-12', ext_options), ('expm', '0.99-1.1', ext_options), ('extrafontdb', '1.0', ext_options), @@ -279,8 +269,9 @@ exts_list = [ ('shapefiles', '0.7', ext_options), ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), + ('labdsv', '1.7-0', ext_options), ('MatrixModels', '0.4-0', ext_options), ('stabs', '0.5-1', ext_options), ('mboost', '2.4-2', ext_options), @@ -288,21 +279,22 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.9', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), ('TH.data', '1.0-6', ext_options), ('multcomp', '1.4-0', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('rms', '4.3-0', ext_options), + ('rms', '4.3-1', ext_options), ('RWekajars', '3.7.12-1', ext_options), ('RWeka', '0.4-24', ext_options), ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), + ('tm', '0.6-2', ext_options), ('TraMineR', '1.8-9', ext_options), ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), - ('statmod', '1.4.20', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), ('maxLik', '1.2-4', ext_options), ('mlogit', '0.2-4', ext_options), @@ -312,81 +304,66 @@ exts_list = [ ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), - ('affyio', '1.34.0', 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'1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), - ('RNASeqPower', '1.6.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('Rsubread', '1.16.1', bioconductor_options), - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk - ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), ] moduleclass = 'lang' - -- GitLab From 00b2748f6387c83f3f49e0b05456c53b821ee0e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 22:33:03 +0200 Subject: [PATCH 0946/1172] add missing libxml2 easyconfig --- .../l/libxml2/libxml2-2.9.2-intel-2015b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb new file mode 100644 index 0000000000..70be4707e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -0,0 +1,28 @@ +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': 'intel', 'version': '2015b'} + +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')] + +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 5b1628029f2af661f66da648163f31feba7bb254 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 22:34:14 +0200 Subject: [PATCH 0947/1172] remove unrequired easyconfig for libpng 1.6.16 w/ foss/2015b --- .../l/libpng/libpng-1.6.16-foss-2015b.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb deleted file mode 100644 index 7d2de2d1c3..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -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': 'foss', 'version': '2015b'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -moduleclass = 'lib' -- GitLab From 1ce02691de5f9b7c38d1af53c7976d22392f519a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 22:46:15 +0200 Subject: [PATCH 0948/1172] {devel,bio}[*/2015b] BLAST+ 2.2.31 + Boost 1.58.0 --- .../BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb | 40 +++++++++++++++++ ...BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb | 43 +++++++++++++++++++ .../Boost-1.58.0-foss-2015b-Python-2.7.10.eb | 25 +++++++++++ .../Boost-1.58.0-intel-2015b-Python-2.7.10.eb | 25 +++++++++++ 4 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..53cded48eb --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.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 , Kenneth Hoste (UGent) +# 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 = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..a150b8d6d9 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# 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 = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..d4ec7f6e79 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..b3c4d08fad --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 183abf94bd4ac2f376a267df57630e3685bfbdf4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 23:17:21 +0200 Subject: [PATCH 0949/1172] fix name of patch file in BLAST+ 2.2.31 easyconfig --- .../b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb index 53cded48eb..a64fc6a528 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb @@ -26,7 +26,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['%(name)s-%(version)s_basename-fixes.patch'] +patches = ['%(name)s-2.2.30_basename-fixes.patch'] dependencies = [('Boost', '1.58.0', versionsuffix)] -- GitLab From d7885982b66396345d9af387bb12b8f314756206 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 23:23:44 +0200 Subject: [PATCH 0950/1172] {chem}[*/2015b] CP2K 2.6.1 + deps --- .../b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.eb | 22 +++++++++++ .../c/CP2K/CP2K-2.6.1-foss-2015b.eb | 38 +++++++++++++++++++ .../c/CP2K/CP2K-2.6.1-intel-2015b.eb | 38 +++++++++++++++++++ .../f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb | 15 ++++++++ .../l/Libint/Libint-1.1.4-foss-2015b.eb | 24 ++++++++++++ .../l/Libint/Libint-1.1.4-intel-2015b.eb | 24 ++++++++++++ .../l/libxc/libxc-2.2.2-foss-2015b.eb | 32 ++++++++++++++++ .../l/libxc/libxc-2.2.2-intel-2015b.eb | 32 ++++++++++++++++ 8 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..22f9944d4d --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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/CP2K/CP2K-2.6.1-foss-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb new file mode 100644 index 0000000000..9aa1e31e3d --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.1' + +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': 'foss', 'version': '2015b'} +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', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), +] + +# 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/c/CP2K/CP2K-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb new file mode 100644 index 0000000000..ec3d535442 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.1' + +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': '2015b'} +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', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), +] + +# 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/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..7c5e4528e0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +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': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb new file mode 100644 index 0000000000..ba9b735bea --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.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': 'foss', 'version': '2015b'} +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/Libint/Libint-1.1.4-intel-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb new file mode 100644 index 0000000000..1e71a38b55 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.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': '2015b'} +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-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb new file mode 100644 index 0000000000..355b1a14f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.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': 'foss', 'version': '2015b'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb new file mode 100644 index 0000000000..b07c35e531 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$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.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 70735ec1fb81e453acbd14088fa731da8fdc46b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Aug 2015 23:43:03 +0200 Subject: [PATCH 0951/1172] remove Intel-specific patches for R libs in R 3.2.1 foss/2015b easyconfig --- easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb index 1528a48e4d..e61ba5e9a5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -53,10 +53,10 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('Rmpi', '0.6-5', ext_options), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('geometry', '0.3-5', ext_options), ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), @@ -341,7 +341,7 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('vegan', '2.3-0', ext_options), - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('forecast', '6.1', ext_options), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), -- GitLab From 91a74b0e2098afb769e00b5fbd2985c404042b74 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 27 Aug 2015 23:01:26 +0100 Subject: [PATCH 0952/1172] Add Boost 1.58 with Python 2.7.10 for intel-2015a --- .../b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb index d48f0872dd..cce9488a73 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -4,7 +4,7 @@ version = '1.58.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 9ebd3eb81fd81d38c8c3f59441d07922185ff242 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 09:48:49 +0200 Subject: [PATCH 0953/1172] fix Java version in R 3.2.1 -bare foss/2015b easyconfig --- easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb index c7ffa781a4..a09dbc1a66 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From f2e389741100afd4b739423fef4c0d191d6b2117 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 09:49:25 +0200 Subject: [PATCH 0954/1172] fix Java version in R 3.2.1 -bare intel/2015b easyconfig --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb index 3fb6481118..427432ba53 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From 113139cd798d322a8fb1eb601bc42a15a911d17d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 28 Aug 2015 10:20:21 +0200 Subject: [PATCH 0955/1172] configopts moved to easyblock --- .../easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 19de9ccda0..15b01d0c7c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -26,15 +26,9 @@ builddependencies = [ ] # make sure both static and shared libs are built -configopts_tmpl = '-DBUILD_SHARED_LIBS={0} -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG " ' -configopts_tmpl += "-DHDF5_LIB=$EBROOTHDF5/lib/libhdf5.so -DHDF5_HL_LIB=$EBROOTHDF5/lib/libhdf5_hl.so " -configopts_tmpl += "-DHDF5_INCLUDE_DIR=$EBROOTHDF5/include " -configopts_tmpl += "-DSZIP_LIBRARY=$EBROOTSZIP/lib/libsz.so " -configopts_tmpl += "-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so " -configopts_tmpl += "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include " configopts = [ - configopts_tmpl.format('OFF'), - configopts_tmpl.format('ON'), + configopts = "-DBUILD_SHARED_LIBS=OFF " + configopts = "-DBUILD_SHARED_LIBS=ON " ] moduleclass = 'data' -- GitLab From 891ee2f248b5c7e8e07db9b082b48bbef7d35830 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 28 Aug 2015 09:48:36 +0100 Subject: [PATCH 0956/1172] Remove superfluous Boost 1.55.0 easyconfigs --- .../Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb | 27 ------------------- .../Boost-1.55.0-intel-2015a-Python-2.7.9.eb | 25 ----------------- 2 files changed, 52 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb deleted file mode 100644 index 349cfa6a3d..0000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'Boost' -version = '1.55.0' - -homepage = 'http://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'pic': True, 'usempi': True} - -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -source_urls = [SOURCEFORGE_SOURCE] - -pythonversion = '2.7.9' -versionsuffix = '-Python-%s' % pythonversion - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('Python', pythonversion), -] - -configopts = '--without-libraries=python' - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb deleted file mode 100644 index 856e218f9f..0000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'Boost' -version = '1.55.0' - -homepage = 'http://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] - -pythonversion = '2.7.9' -versionsuffix = '-Python-%s' % pythonversion - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('Python', pythonversion), -] - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' -- GitLab From 21429bd39b22ca8a40f40ac4828ac304b1731572 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 28 Aug 2015 09:55:01 +0100 Subject: [PATCH 0957/1172] Remove unnecessary space --- .../b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb index cce9488a73..d48f0872dd 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -4,7 +4,7 @@ version = '1.58.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 0516b7f8c619372a6029f529c05e13dc0149a8b2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 28 Aug 2015 10:59:14 +0200 Subject: [PATCH 0958/1172] missing commas added --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 15b01d0c7c..81d94b3eb0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -27,8 +27,8 @@ builddependencies = [ # make sure both static and shared libs are built configopts = [ - configopts = "-DBUILD_SHARED_LIBS=OFF " - configopts = "-DBUILD_SHARED_LIBS=ON " + configopts = "-DBUILD_SHARED_LIBS=OFF ", + configopts = "-DBUILD_SHARED_LIBS=ON ", ] moduleclass = 'data' -- GitLab From 2c5496a22372b70add33a5aa907e836de3b52e83 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 28 Aug 2015 11:01:18 +0200 Subject: [PATCH 0959/1172] syntax corrected --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index 81d94b3eb0..ee5055dfe4 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -27,8 +27,8 @@ builddependencies = [ # make sure both static and shared libs are built configopts = [ - configopts = "-DBUILD_SHARED_LIBS=OFF ", - configopts = "-DBUILD_SHARED_LIBS=ON ", + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", ] moduleclass = 'data' -- GitLab From b444327bebe9994326684b65e69028fbe3a381fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 11:12:50 +0200 Subject: [PATCH 0960/1172] exclude cyclink symlink files when unpacking OpenFOAM 2.3.1 --- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb | 6 ++++++ .../easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb index 24739eaae8..645bcba351 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb @@ -21,6 +21,12 @@ patches = [ ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + dependencies = [ ('libreadline', '6.3'), ('SCOTCH', '6.0.4'), diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb index 3c1706af3a..944836d77d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb @@ -21,6 +21,12 @@ patches = [ ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + dependencies = [ ('libreadline', '6.3'), ('SCOTCH', '6.0.4'), -- GitLab From 5f40930caec756f4ad058ed14c6d58b6271bff2a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 28 Aug 2015 10:42:53 +0100 Subject: [PATCH 0961/1172] Removed commented out Python option --- .../b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb index 5118cf95ff..dba26f94f4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb @@ -19,8 +19,6 @@ dependencies = [ ('Python', pythonversion), ] -#configopts = '--without-libraries=python' - # also build boost_mpi boost_mpi = True -- GitLab From bda13da0de01075847dcc8f7ee0c2190020154ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 13:56:02 +0200 Subject: [PATCH 0962/1172] {tools}[GCC/4.9.2] parallel 20150822 --- .../p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb | 17 ++++++++++++++ .../p/parallel/parallel-20150822-GCC-4.9.2.eb | 23 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000..cff5256c81 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb new file mode 100644 index 0000000000..c57168e629 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20150822' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/parallel'] + +dependencies = [ + ('Perl', '5.22.0', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 1616ee4d3507c144e88cd07e23220c45f91c2da3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 14:05:55 +0200 Subject: [PATCH 0963/1172] add --exclude unpack options for OpenFOAM 2.3.1 to dancy around cyclic symlink causing problems when unpacking --- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 6 ++++++ .../easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 9e1b2ca02b..4055b16ed1 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -21,6 +21,12 @@ patches = [ ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + dependencies = [ ('libreadline', '6.3'), ('SCOTCH', '6.0.4'), diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb index 06ceafc8c9..5eecb4a977 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb @@ -21,6 +21,12 @@ patches = [ ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + dependencies = [ ('libreadline', '6.3'), ('SCOTCH', '6.0.4'), -- GitLab From 3bfa8207bf4691e291de9484706b379df68a462d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Aug 2015 15:44:14 +0200 Subject: [PATCH 0964/1172] use GNU_SOURCE --- easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb index c57168e629..cd915dedbc 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb @@ -9,7 +9,7 @@ description = """parallel: Build and execute shell commands in parallel""" toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/parallel'] +source_urls = [GNU_SOURCE] dependencies = [ ('Perl', '5.22.0', '-bare'), -- GitLab From 1d42ea6f4a4637b02f7e2e94ebd0fc7d38bf686a Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 31 Aug 2015 11:10:59 +0200 Subject: [PATCH 0965/1172] Add SOAPdenovo2-r240-intel-2015a.eb --- .../SOAPdenovo2-r240-intel-2015a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb new file mode 100644 index 0000000000..1761063fd7 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb @@ -0,0 +1,40 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r240' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3c35ea8ad9822e46fea69a0fa784a8596d987bb5 Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 31 Aug 2015 11:45:22 +0200 Subject: [PATCH 0966/1172] add ABySS-1.3.7-intel-2015a-Python-2.7.9.eb --- .../ABySS-1.3.7-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb 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 new file mode 100644 index 0000000000..0cb2691894 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.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 +# 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_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.3.7' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] + } + +moduleclass = 'bio' -- GitLab From 54f5113b3945d1ea6fe2c7e81edd10fa8355b305 Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 31 Aug 2015 13:48:36 +0200 Subject: [PATCH 0967/1172] add sparsehash dep to ABySS-1.3.7-intel-2015a-Python-2.7.9.eb --- .../a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 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 0cb2691894..20c30c8e62 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 @@ -26,11 +26,16 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] -dependencies = [('Boost', '1.58.0', versionsuffix)] +dependencies = [ + ('sparsehash', '2.0.2'), + ('Boost', '1.58.0', versionsuffix), +] + +preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' -- GitLab From cf22edc1b2d2d77669d5f74a85b424a4e7869c2f Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 31 Aug 2015 14:15:22 +0200 Subject: [PATCH 0968/1172] add Oases-0.2.08-intel-2015a.eb --- .../o/Oases/Oases-0.2.08-intel-2015a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb new file mode 100644 index 0000000000..6313565ba1 --- /dev/null +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.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 , Fotis Georgatos +# License:: MIT/GPL +# +## + +easyblock = "MakeCp" + +name = 'Oases' +version = '0.2.08' + +homepage = 'http://www.ebi.ac.uk/~zerbino/oases/' +description = """Oases is a de novo transcriptome assembler designed to produce transcripts from + short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +velvetver = '1.2.09' + +sources = [ + '%(namelower)s_%(version)s.tgz', + 'velvet_%s.tgz' % velvetver, +] + +source_urls = [ + 'http://www.ebi.ac.uk/~zerbino/%(namelower)s', + 'http://www.ebi.ac.uk/~zerbino/velvet', +] + +# listed make targets exclude 'doc' on purpose +buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] + +files_to_copy = [(["oases"],'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] + +sanity_check_paths={ + 'files': ["bin/oases", "LICENSE.txt", "README.txt"], + 'dirs': ["data", "scripts", "src", "doc"] +} + +parallel = 1 + +moduleclass = 'bio' -- GitLab From 0e3e7b55b7fa6c10d2a7d33b747e56d642d8ebda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Aug 2015 16:24:28 +0200 Subject: [PATCH 0969/1172] {tools}[GCC/4.9.2] p7zip 9.38.1 --- .../p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..df547ff87f --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '9.38.1' + +homepage = 'http://p7zip.sourceforge.net/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. + 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['p7zip_%(version)s_src_all.tar.bz2'] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'bin/7z.so', 'bin/Codecs/Rar29.so'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 381377a1daef8271da52e05003c3b4c2c1b00424 Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 31 Aug 2015 16:28:50 +0200 Subject: [PATCH 0970/1172] add DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb and dep j/jemalloc/jemalloc-3.6.0-foss-2015a.eb --- .../DISCOVARdenovo-52488-foss-2015a.eb | 22 ++++++++++++++++++ .../j/jemalloc/jemalloc-3.6.0-foss-2015a.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb new file mode 100644 index 0000000000..ba529d60cc --- /dev/null +++ b/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb @@ -0,0 +1,22 @@ +name = 'DISCOVARdenovo' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/discovar/blog/' +description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code'] + +dependencies = [ + ('GMP', '6.0.0a'), + ('jemalloc', '3.6.0'), +] + +sanity_check_paths = { + 'files': ["bin/AffineAlign"], + 'dirs': ["bin","share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb new file mode 100644 index 0000000000..b9fa570529 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '3.6.0' + +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': 'foss', 'version': '2015a'} + +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.so', + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + +moduleclass = 'lib' -- GitLab From 422b3d543bab4e2617cef2708fc04de2abcc2b17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Aug 2015 17:13:55 +0200 Subject: [PATCH 0971/1172] define alias for '7z' --- easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb index df547ff87f..ffb7f9351e 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb @@ -22,4 +22,8 @@ sanity_check_paths = { 'dirs': [], } +# 7z must be called full path in order to avoid problem with 7z.so not being found +# cfr. http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +modaliases = {'7z': '%(installdir)s/bin/7z'} + moduleclass = 'tools' -- GitLab From 5927af52a91c9e1b731ad3286525305b322f5f9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Aug 2015 18:53:27 +0200 Subject: [PATCH 0972/1172] create wrapper script rather than alias for 7z --- .../p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb | 20 ++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb index ffb7f9351e..6f10745d26 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb @@ -15,15 +15,21 @@ sources = ['p7zip_%(version)s_src_all.tar.bz2'] prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' -files_to_copy = ['bin'] +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod a+x %(installdir)s/bin/7z", +] sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'bin/7z.so', 'bin/Codecs/Rar29.so'], - 'dirs': [], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], } -# 7z must be called full path in order to avoid problem with 7z.so not being found -# cfr. http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ -modaliases = {'7z': '%(installdir)s/bin/7z'} - moduleclass = 'tools' -- GitLab From 95ba00e85152bc2b381f0217aeb48af30e2bbe5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Sep 2015 10:00:55 +0200 Subject: [PATCH 0973/1172] fix chmod, add sanity check commands for 7z --- easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb index 6f10745d26..aba7c4da3f 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb @@ -24,7 +24,7 @@ files_to_copy = [ # see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ postinstallcmds = [ "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", - "chmod a+x %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask ] sanity_check_paths = { @@ -32,4 +32,10 @@ sanity_check_paths = { 'dirs': ['libexec/Codecs'], } +# check whether 7z script works +sanity_check_commands = [ + ('7z', '--help'), # print help, exit 0 + ('7z', "x || test $? -gt 0"), # missing argument, exit code > 0 +] + moduleclass = 'tools' -- GitLab From 34d2692ce868d36654eb92f594e6461fc09ab2b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Sep 2015 10:21:59 +0200 Subject: [PATCH 0974/1172] add p7zip easyconfig with dummy toolchain --- easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb new file mode 100644 index 0000000000..b709c55a99 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '9.38.1' + +homepage = 'http://p7zip.sourceforge.net/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. + 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['p7zip_%(version)s_src_all.tar.bz2'] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], +} + +# check whether 7z script works +sanity_check_commands = [ + ('7z', '--help'), # print help, exit 0 + ('7z', "x || test $? -gt 0"), # missing argument, exit code > 0 +] + +moduleclass = 'tools' -- GitLab From e90fbcf6e6df0b2712e17ad6230c608dd5ccbdc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Sep 2015 20:50:50 +0200 Subject: [PATCH 0975/1172] bump version to 2.3.0 and update release notes --- RELEASE_NOTES | 29 ++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 7d3ae9ed16..9239dd7b22 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,36 @@ 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 4,061 easyconfig files, for 673 different software packages, +The latest version of easybuild-easyconfig provides 4,260 easyconfig files, for 692 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +v2.3.0 (September 2nd 2015) +--------------------------- + +feature + bugfix release +- added example easyconfig files for 19 new software packages: + ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780), + gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677), Molpro (#1880), + NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859) +- added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696) + add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, + Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0 +- various other enhancements, including: + - enhance texinfo easyconfig w.r.t. texmf, only use it as a build dependency (#1840) + - enable building of ld.gold in binutils 2.25 (#1885) +- various bug fixes, including: + - fix enabling MPI support for h5py 2.5.0 (#1825) + - fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917) + - put dummly values in place for builddir/installdir templates in easyconfigs unit tests (#1835) + - fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875) + - add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858) + - specify installation prefix for SIP (#1888, #1892) + - add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909) + - don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911) + - add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925) + v2.2.0 (July 15th 2015) ----------------------- diff --git a/setup.py b/setup.py index d3563514ac..b97bf4217c 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.3.0dev' +VERSION = '2.3.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c1f045e7b5e700b2e79260af0df7ba3364e72e22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 07:33:23 +0200 Subject: [PATCH 0976/1172] fix typo --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9239dd7b22..ac32bc392c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -25,7 +25,7 @@ feature + bugfix release - various bug fixes, including: - fix enabling MPI support for h5py 2.5.0 (#1825) - fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917) - - put dummly values in place for builddir/installdir templates in easyconfigs unit tests (#1835) + - put dummy values in place for builddir/installdir templates in easyconfigs unit tests (#1835) - fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875) - add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858) - specify installation prefix for SIP (#1888, #1892) -- GitLab From 8b13b70299c4d74815892e689842ef41c5bb33a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 07:35:19 +0200 Subject: [PATCH 0977/1172] fix long line --- RELEASE_NOTES | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index ac32bc392c..e9755b2740 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -12,8 +12,8 @@ v2.3.0 (September 2nd 2015) feature + bugfix release - added example easyconfig files for 19 new software packages: ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780), - gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677), Molpro (#1880), - NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859) + gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677), + Molpro (#1880), NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859) - added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696) add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1 -- GitLab From 517080dcca1820184ae90a442eb7b683e2744644 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 08:21:06 +0200 Subject: [PATCH 0978/1172] mention list of software names for which custom sanity check paths needed to be added in easyconfigs --- RELEASE_NOTES | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e9755b2740..13ba90be8d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -30,6 +30,12 @@ feature + bugfix release - add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858) - specify installation prefix for SIP (#1888, #1892) - add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909) + - required because of fix in EasyBuild framework, causing default sanity check paths to be considered + for extensions that are installed as a module + - affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql, + evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx, + ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn, + SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck - don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911) - add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925) -- GitLab From 4c7056c5af7b9ce39df6b329ef0735ed071920d7 Mon Sep 17 00:00:00 2001 From: molden Date: Wed, 2 Sep 2015 09:35:24 +0200 Subject: [PATCH 0979/1172] add MIRA-4.0.2-foss-2015a-Python-2.7.9.eb and deps --- .../g/gperftools/gperftools-2.4-foss-2015a.eb | 28 +++++++++++++++ .../l/libunwind/libunwind-1.1-foss-2015a.eb | 23 ++++++++++++ .../MIRA-4.0.2-foss-2015a-Python-2.7.9.eb | 35 +++++++++++++++++++ .../m/MIRA/MIRA-4.0.2-quirks.patch | 13 +++++++ 4 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb new file mode 100644 index 0000000000..e0e0ffda47 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.4" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +dependencies = [ + ('Automake', '1.15','',('GCC', '4.9.2')), + ('Autoconf', '2.69','',('GCC', '4.9.2')), + ('libtool', '2.4.5','',('GCC', '4.9.2')), + ('libunwind', '1.1'), +] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb new file mode 100644 index 0000000000..74be1e3d78 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.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 = {'version': '2015a', 'name': 'foss'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..61f1e2469d --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +name = 'MIRA' +version = '4.0.2' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] + +configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' + +patches = ['MIRA-%(version)s-quirks.patch'] + +dependencies = [ + ('Boost', '1.58.0',versionsuffix), + ('expat', '2.1.0'), + ('zlib', '1.2.8'), + ('flex', '2.5.39'), + ('gperftools', '2.4'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin","share"], +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch new file mode 100644 index 0000000000..062ec9454f --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch @@ -0,0 +1,13 @@ +# solve error reported: https://github.com/Homebrew/homebrew-science/issues/2268 +# +--- a/src/progs/quirks.C.old ++++ b/src/progs/quirks.C +@@ -22,7 +22,7 @@ + * + */ + +- ++#include + #include + + // make the "tcmalloc: large alloc" messages from TCMallom disappear -- GitLab From 81db0fb4857fdab0435d90d8d49fb95a3dbb6fd0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Sep 2015 11:20:59 +0200 Subject: [PATCH 0980/1172] Rosetta upgrade --- .../SCons-2.3.6-intel-2015a-Python-2.7.9.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..eaa34798de --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +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 2a474036858fa803e2d7b7e96f866bfc760422fd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Sep 2015 11:21:24 +0200 Subject: [PATCH 0981/1172] Rosetta upgrade2 --- .../Rosetta/Rosetta-2015.31.58019-intel-2015a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb new file mode 100644 index 0000000000..64d1ea29a2 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb @@ -0,0 +1,16 @@ +name = 'Rosetta' +version = '2015.31.58019' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 1b85a962ffc2e2754784dd5661d404661b30291c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 2 Sep 2015 11:27:39 +0200 Subject: [PATCH 0982/1172] ROSETTA3_DB environmental variable added --- .../r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb index 64d1ea29a2..10b2a8fd9c 100644 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb @@ -13,4 +13,8 @@ sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + moduleclass = 'bio' -- GitLab From 16ef15b207ad766711020a217413f5c055a6ad02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 13:03:06 +0200 Subject: [PATCH 0983/1172] bump version to 2.3.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b97bf4217c..ca10696d02 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.3.0' +VERSION = '2.3.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From ffa50153179e53a8b9e92c55936ba82b8ad13071 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 13:03:49 +0200 Subject: [PATCH 0984/1172] bump version to 2.4.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ca10696d02..5d2a2c7ab6 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.3.1dev' +VERSION = '2.4.0dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 28f1827b77eadc6edc5e8b9c5cff5af74c11bd34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 14:23:40 +0200 Subject: [PATCH 0985/1172] {tools}[dummy] EasyBuild 2.3.0 --- .../e/EasyBuild/EasyBuild-2.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb new file mode 100644 index 0000000000..6080ef8f0c --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.3.0' + +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-2.2.4.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 ae5c12cded254f4bc7b78be63e4d97fba3d8d8a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 16:05:37 +0200 Subject: [PATCH 0986/1172] {cae}[dummy] Samcef 17.0-03 --- easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb diff --git a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb new file mode 100644 index 0000000000..3504977eb7 --- /dev/null +++ b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb @@ -0,0 +1,14 @@ +name = 'Samcef' +version = '17.0-03' + +homepage = 'http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/' +description = """FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and + thermal applications.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# licensed software, no source URls for automatic download +# note: unpacking requires that 7z (p7zip) is available +sources = ['SamcefV17.0-03.iso'] + +moduleclass = 'cae' -- GitLab From f33af472da62a7864592a266efee144a9294297f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2015 17:22:15 +0200 Subject: [PATCH 0987/1172] don't hardwire Samcef version in sources --- easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb index 3504977eb7..7464a3d289 100644 --- a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb +++ b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb @@ -9,6 +9,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # licensed software, no source URls for automatic download # note: unpacking requires that 7z (p7zip) is available -sources = ['SamcefV17.0-03.iso'] +sources = ['SamcefV%(version)s.iso'] moduleclass = 'cae' -- GitLab From 54936d57163b59efd560e5587bb3a82ea20684fd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Sep 2015 11:29:36 +0200 Subject: [PATCH 0988/1172] {bio} [intel-2015a] MIGRATE-N (REVIEW) --- .../MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb | 39 +++++++++++++++++++ .../m/MIGRATE-N/migrate-3.6.11_icc.patch | 13 +++++++ .../m/MIGRATE-N/migrate-3.6.11_install.patch | 13 +++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb new file mode 100644 index 0000000000..33a96243d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb @@ -0,0 +1,39 @@ +easyblock = "ConfigureMake" + +name = "MIGRATE-N" +version = "3.6.11" + +homepage = 'http://popgen.sc.fsu.edu/Migrate/Migrate-n.html' +description = """Migrate estimates effective population sizes and past migration rates + between n population assuming a migration matrix model + with asymmetric migration tates and different subpopulation sizes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://popgen.sc.fsu.edu/currentversions/', + 'http://popgen.sc.fsu.edu/oldversions/%(version_major)s.x/%(version_major_minor)s', + 'http://popgen.sc.fsu.edu/oldversions/', +] +sources = ['migrate-%(version)s.src.tar.gz'] + +patches = [ + 'migrate-%(version)s_icc.patch', + 'migrate-%(version)s_install.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-A4 CC=icc ' +prebuildopts = 'make mpis && make clean && ' + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/migrate-n', 'bin/migrate-n-mpi'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch new file mode 100644 index 0000000000..5c06ee45aa --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch @@ -0,0 +1,13 @@ +#icc does not find -lpthread, if -fast defined +#B. Hajgato 3rd September 2015 +--- src/configure.old 2015-05-02 14:42:10.000000000 +0200 ++++ src/configure 2015-09-03 10:00:54.320014335 +0200 +@@ -3333,7 +3333,7 @@ + pgcc) CFLAGS="-B -fast "; + SYSTEM="gcc";; + # icc) CFLAGS=" -O3 -tpp7 -xKW -pad -ip "; +- icc) CFLAGS+=" -fast "; ++ icc) CFLAGS+=""; + SYSTEM="icc";; + cc) case "$host_vendor" in + ibm) CFLAGS="-O3 -Dinline='/*inline*/' -q cpluscmt -DIBM"; diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch new file mode 100644 index 0000000000..77600f365c --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch @@ -0,0 +1,13 @@ +#Create parent directories during install +#B. Hajgato 3rd September 2015 +--- src/configure.old 2015-05-02 14:42:10.000000000 +0200 ++++ src/configure 2015-09-03 10:00:54.320014335 +0200 +@@ -3412,7 +3412,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi -- GitLab From 1e09d750687e2f0f22138ceb46f61f421ca571a2 Mon Sep 17 00:00:00 2001 From: molden Date: Thu, 3 Sep 2015 14:13:34 +0200 Subject: [PATCH 0989/1172] minor style fixes --- easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb index 6313565ba1..9c657fda4a 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb @@ -32,14 +32,13 @@ source_urls = [ # listed make targets exclude 'doc' on purpose buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] +parallel = 1 -files_to_copy = [(["oases"],'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] sanity_check_paths={ 'files': ["bin/oases", "LICENSE.txt", "README.txt"], 'dirs': ["data", "scripts", "src", "doc"] } -parallel = 1 - moduleclass = 'bio' -- GitLab From 7645f8b909ffa65fb1e026fe438e46d2ad55cf85 Mon Sep 17 00:00:00 2001 From: molden Date: Thu, 3 Sep 2015 14:21:40 +0200 Subject: [PATCH 0990/1172] rename folder --- .../DISCOVARdenovo-52488-foss-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb diff --git a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb new file mode 100644 index 0000000000..ba529d60cc --- /dev/null +++ b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb @@ -0,0 +1,22 @@ +name = 'DISCOVARdenovo' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/discovar/blog/' +description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code'] + +dependencies = [ + ('GMP', '6.0.0a'), + ('jemalloc', '3.6.0'), +] + +sanity_check_paths = { + 'files': ["bin/AffineAlign"], + 'dirs': ["bin","share"], +} + +moduleclass = 'bio' -- GitLab From 87cd2781a74818ba494b9f7fe9fd525a842fc5e3 Mon Sep 17 00:00:00 2001 From: molden Date: Thu, 3 Sep 2015 14:28:01 +0200 Subject: [PATCH 0991/1172] minor style fixes --- .../d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb index ba529d60cc..5f9ea822ee 100644 --- a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb +++ b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb @@ -1,12 +1,15 @@ +easyblock = 'ConfigureMake' + name = 'DISCOVARdenovo' version = '52488' homepage = 'http://www.broadinstitute.org/software/discovar/blog/' -description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.""" +description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. + It currently does not call variants.""" toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code'] dependencies = [ -- GitLab From fb16b26b0d6560eedb559c1bf4255c484267fa1c Mon Sep 17 00:00:00 2001 From: molden Date: Thu, 3 Sep 2015 14:36:29 +0200 Subject: [PATCH 0992/1172] minor style fixes --- .../g/gperftools/gperftools-2.4-foss-2015a.eb | 6 +++--- .../m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb | 10 ++++++---- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb index e0e0ffda47..18319be734 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb @@ -14,9 +14,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] dependencies = [ - ('Automake', '1.15','',('GCC', '4.9.2')), - ('Autoconf', '2.69','',('GCC', '4.9.2')), - ('libtool', '2.4.5','',('GCC', '4.9.2')), + ('Automake', '1.15','', ('GCC', '4.9.2')), + ('Autoconf', '2.69','', ('GCC', '4.9.2')), + ('libtool', '2.4.5','', ('GCC', '4.9.2')), ('libunwind', '1.1'), ] diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb index 61f1e2469d..df81cb2c80 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'MIRA' version = '4.0.2' versionsuffix = '-Python-2.7.9' @@ -6,20 +8,20 @@ homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" -# don't use PAX, it might break. -tar_config_opts = True - toolchain = {'name': 'foss', 'version': '2015a'} sources = ['%(namelower)s-%(version)s.tar.bz2'] source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] +# don't use PAX, it might break. +tar_config_opts = True + configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' patches = ['MIRA-%(version)s-quirks.patch'] dependencies = [ - ('Boost', '1.58.0',versionsuffix), + ('Boost', '1.58.0', versionsuffix), ('expat', '2.1.0'), ('zlib', '1.2.8'), ('flex', '2.5.39'), -- GitLab From 3cc6ad470fb0e3b1918819d0fd34e462064318c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Sep 2015 12:02:45 +0200 Subject: [PATCH 0993/1172] {chem}[intel/2015a] PLUMED 2.1.3 --- .../p/PLUMED/PLUMED-2.1.3-intel-2015a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb new file mode 100644 index 0000000000..a7478b0842 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -0,0 +1,33 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.1.3' + +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': '2015a'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['PLUMED-2.0.4_eb-env-vars.patch'] + +preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' -- GitLab From 11b1de01e5eed7ca839d954aaf37e81976b904c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Sep 2015 12:13:05 +0200 Subject: [PATCH 0994/1172] remove nasty hack of commenting out actual configure command --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb | 4 +++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb index b6955fcdcc..e6ac2070ea 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -20,7 +20,9 @@ sources = ['v%(version)s.tar.gz'] patches = ['PLUMED-%(version)s_eb-env-vars.patch'] -preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +skipsteps = ['configure'] + +prebuildopts = " ./configure.sh linux.icc && source sourceme.sh && " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb index a7478b0842..3b3039884a 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -20,7 +20,9 @@ sources = ['v%(version)s.tar.gz'] patches = ['PLUMED-2.0.4_eb-env-vars.patch'] -preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +skipsteps = ['configure'] + +prebuildopts = " ./configure.sh linux.icc && source sourceme.sh && " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " sanity_check_paths = { -- GitLab From 427784928ef776af7aecd255a01f668864f4f096 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Sep 2015 17:18:28 +0200 Subject: [PATCH 0995/1172] CP2K of today with PLUMED support --- .../CP2K/CP2K-20150904-intel-2015a-PLUMED.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb new file mode 100644 index 0000000000..3fe7724ff9 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb @@ -0,0 +1,41 @@ +name = 'CP2K' +version = '20150904' +versionsuffix = '-PLUMED' + +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': '2015a'} +toolchainopts = {'pic': True} + +# we use the git mirror: this is r15816 or 68331ef35b7 +sources = ['68331ef35b7.zip'] +source_urls = ['https://github.com/cp2k/cp2k/archive/'] + +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', '2.2.1'), + ('PLUMED', '2.1.3'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# 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' -- GitLab From 6749a0130612135276c441104d15aece3b4ca347 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Sep 2015 17:25:33 +0200 Subject: [PATCH 0996/1172] Actually use PLUMED now --- ...-PLUMED.eb => CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb} | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/CP2K/{CP2K-20150904-intel-2015a-PLUMED.eb => CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb} (86%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb similarity index 86% rename from easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb rename to easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index 3fe7724ff9..15a54f9bc6 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -1,6 +1,6 @@ name = 'CP2K' version = '20150904' -versionsuffix = '-PLUMED' +versionsuffix = '-PLUMED-2.1.3' homepage = 'http://www.cp2k.org/' description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular @@ -31,9 +31,7 @@ builddependencies = [ ('Bison', '3.0.2'), ] -# don't use parallel make, results in compilation failure -# because Fortran module files aren't created before they are needed -parallel = 1 +plumed = True # regression test reports failures ignore_regtest_fails = True -- GitLab From c49145feccd648aa858a24ca3313f092f1472880 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Sep 2015 17:44:01 +0200 Subject: [PATCH 0997/1172] Specify patch directory for CP2k patch --- .../c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index 15a54f9bc6..34744178b8 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -16,7 +16,7 @@ sources = ['68331ef35b7.zip'] source_urls = ['https://github.com/cp2k/cp2k/archive/'] patches = [ - 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + ('CP2K-2.6.0-ifort-compiler-bug-fix.patch', 'cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/'), 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -- GitLab From a284bf9b56e8334d23628f8f5c127c6dba8d1056 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Sep 2015 18:19:09 +0200 Subject: [PATCH 0998/1172] Fixed patch for CP2K --- .../CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch | 13 +++++++++++++ .../CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 2 +- 2 files changed, 14 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch new file mode 100644 index 0000000000..42ccd853c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch @@ -0,0 +1,13 @@ +# workaround for ifort bug +# https://groups.google.com/forum/#!topic/cp2k/LorI2Z4pQgc +diff -ur cp2k-68331ef35b7890a8b05b9111660f57863af14df0.orig/cp2k/src/dbcsr/error/dbcsr_error_handling.F cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/src/dbcsr/error/dbcsr_error_handling.F +--- cp2k-68331ef35b7890a8b05b9111660f57863af14df0.orig/cp2k/src/dbcsr/error/dbcsr_error_handling.F 2015-09-04 15:29:57.000000000 +0200 ++++ cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/src/dbcsr/error/dbcsr_error_handling.F 2015-09-04 17:37:48.000000000 +0200 +@@ -20,7 +20,6 @@ + !$ USE OMP_LIB, ONLY: omp_get_max_threads, omp_get_thread_num, omp_get_num_threads + + IMPLICIT NONE +- PRIVATE + + ! procedures + PUBLIC :: dbcsr_error_set, dbcsr_error_stop diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index 34744178b8..8f0372621e 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -16,7 +16,7 @@ sources = ['68331ef35b7.zip'] source_urls = ['https://github.com/cp2k/cp2k/archive/'] patches = [ - ('CP2K-2.6.0-ifort-compiler-bug-fix.patch', 'cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/'), + 'CP2K-%(verion)s-ifort-compiler-bug-fix.patch', 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -- GitLab From 8338e660f3f0bd82e3ce47950e9e247794782f99 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 4 Sep 2015 18:23:26 +0200 Subject: [PATCH 0999/1172] Fix typo --- .../c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index 8f0372621e..c8c01fe2ca 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -16,7 +16,7 @@ sources = ['68331ef35b7.zip'] source_urls = ['https://github.com/cp2k/cp2k/archive/'] patches = [ - 'CP2K-%(verion)s-ifort-compiler-bug-fix.patch', + 'CP2K-%(version)s-ifort-compiler-bug-fix.patch', 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -- GitLab From c0d92a4bc7bc8321b84f613932ba0db4f4675f1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Sep 2015 23:49:20 +0200 Subject: [PATCH 1000/1172] fix double empty line --- easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb index d06010de6a..71bd908a45 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb @@ -3,7 +3,6 @@ easyblock = "CMakeMake" name = "GMT" version = "5.1.2" - homepage = 'http://gmt.soest.hawaii.edu/' description = """GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, -- GitLab From 05c26d2fcf7bb8e8b74416f4a19804e54815d428 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 6 Sep 2015 23:05:20 +0100 Subject: [PATCH 1001/1172] Add BEDTools 2.25.0 for goolf 1.7.20 --- .../BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..dd1aec5c92 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +# 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 9774d636040ef2f785fa10645a4d8108ad76b8bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Sep 2015 07:56:48 +0200 Subject: [PATCH 1002/1172] use Autotools + builddependencies, style/whitespace fixes --- .../g/gperftools/gperftools-2.4-foss-2015a.eb | 8 ++------ .../m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb | 15 +++++++-------- 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb index 18319be734..49065c9ee9 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb @@ -13,12 +13,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] -dependencies = [ - ('Automake', '1.15','', ('GCC', '4.9.2')), - ('Autoconf', '2.69','', ('GCC', '4.9.2')), - ('libtool', '2.4.5','', ('GCC', '4.9.2')), - ('libunwind', '1.1'), -] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +dependencies = [('libunwind', '1.1')] sanity_check_paths = { 'files': ["bin/pprof"], diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb index df81cb2c80..922c0e05ab 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb @@ -2,10 +2,10 @@ easyblock = 'ConfigureMake' name = 'MIRA' version = '4.0.2' -versionsuffix = '-Python-2.7.9' +versionsuffix = '-Python-2.7.9' homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' -description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" toolchain = {'name': 'foss', 'version': '2015a'} @@ -20,18 +20,17 @@ configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' patches = ['MIRA-%(version)s-quirks.patch'] +builddependencies = [('flex', '2.5.39')] dependencies = [ ('Boost', '1.58.0', versionsuffix), ('expat', '2.1.0'), ('zlib', '1.2.8'), - ('flex', '2.5.39'), ('gperftools', '2.4'), ] -sanity_check_paths = { - 'files': ["bin/mira"], - 'dirs': ["bin","share"], -} - +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin", "share"], +} moduleclass = 'bio' -- GitLab From f2c4df7f4737609c375704cff83a668f9e839e79 Mon Sep 17 00:00:00 2001 From: Carlos Fenoy Date: Mon, 7 Sep 2015 18:11:06 +0200 Subject: [PATCH 1003/1172] Added new Go versions. 1.4.2 is needed to build 1.5, as the new versions can only be built with Go compilers. 1.4.2 is the latest version that can be compiled with gcc --- .../easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb | 21 +++++++++++++++++ .../easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb | 23 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb b/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb new file mode 100644 index 0000000000..ef95adc2ea --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb @@ -0,0 +1,21 @@ +# Author: Carlos Fenoy +# F. Hoffmann - La Roche + +name = 'Go' +version = '1.4.2' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = ['%(namelower)s%(version)s.src.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'include', 'pkg'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb new file mode 100644 index 0000000000..dc898cb712 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb @@ -0,0 +1,23 @@ +# Author: Carlos Fenoy +# F. Hoffmann - La Roche + +name = 'Go' +version = '1.5' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = ['%(namelower)s%(version)s.src.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +dependencies = [('Go', '1.4.2')] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +moduleclass = 'compiler' -- GitLab From 62f41fed2ddace163fba45b70c1c459ec847ae15 Mon Sep 17 00:00:00 2001 From: Carles Fenoy Date: Tue, 8 Sep 2015 10:34:46 +0200 Subject: [PATCH 1004/1172] Update Go-1.5-GCC-4.8.4.eb changed dependencies to builddependencies --- easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb index dc898cb712..a5378d6f2f 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = ['%(namelower)s%(version)s.src.tar.gz'] source_urls = ['https://storage.googleapis.com/golang/'] -dependencies = [('Go', '1.4.2')] +builddependencies = [('Go', '1.4.2')] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], -- GitLab From 3ba485f2e37f67612a4cb8e14b28bda867699876 Mon Sep 17 00:00:00 2001 From: molden Date: Tue, 8 Sep 2015 10:38:03 +0200 Subject: [PATCH 1005/1172] delete DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb --- .../DISCOVARdenovo-52488-foss-2015a.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb diff --git a/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb deleted file mode 100644 index ba529d60cc..0000000000 --- a/easybuild/easyconfigs/d/DISCOVAR/DISCOVARdenovo-52488-foss-2015a.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'DISCOVARdenovo' -version = '52488' - -homepage = 'http://www.broadinstitute.org/software/discovar/blog/' -description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = ['%(namelower)s-%(version)s.tar.gz'] -source_urls = ['ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code'] - -dependencies = [ - ('GMP', '6.0.0a'), - ('jemalloc', '3.6.0'), -] - -sanity_check_paths = { - 'files': ["bin/AffineAlign"], - 'dirs': ["bin","share"], -} - -moduleclass = 'bio' -- GitLab From d410156f421dbe1c0fc81760a49ad6660700ab03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2015 09:19:19 +0200 Subject: [PATCH 1006/1172] add easyconfig for GNU time --- easybuild/easyconfigs/t/time/time-1.7.eb | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/time/time-1.7.eb diff --git a/easybuild/easyconfigs/t/time/time-1.7.eb b/easybuild/easyconfigs/t/time/time-1.7.eb new file mode 100644 index 0000000000..215fb8460e --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.7.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.7' + +homepage = 'http://www.gnu.org/software/time/' +description = """iThe `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From dfb368336626ffc58b6f2dbf1f751d994e078eb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2015 09:24:33 +0200 Subject: [PATCH 1007/1172] fix typo --- easybuild/easyconfigs/t/time/time-1.7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/time/time-1.7.eb b/easybuild/easyconfigs/t/time/time-1.7.eb index 215fb8460e..1c4c940235 100644 --- a/easybuild/easyconfigs/t/time/time-1.7.eb +++ b/easybuild/easyconfigs/t/time/time-1.7.eb @@ -4,7 +4,7 @@ name = 'time' version = '1.7' homepage = 'http://www.gnu.org/software/time/' -description = """iThe `time' command runs another program, then displays information about the resources used by that +description = """The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 8d8af471c3d598bfe881b1617939297ef45ba842 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Sep 2015 10:43:59 +0200 Subject: [PATCH 1008/1172] added NFFT for cray --- .../n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..220a53686c --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 91fa117722977e4f23581d49c1cfeab93aad5d09 Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Sep 2015 11:22:21 +0200 Subject: [PATCH 1009/1172] fix dynamic toolchainopts NFFT for cray --- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb index 220a53686c..dca0868591 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb @@ -9,6 +9,7 @@ description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fa dimensions, of arbitrary input size, and of complex data.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = { 'dynamic': True } source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0b39cecb7924faeab6aba8473af04383ec360daf Mon Sep 17 00:00:00 2001 From: perettig Date: Wed, 9 Sep 2015 12:05:24 +0200 Subject: [PATCH 1010/1172] added spglib for cray --- .../s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..2e71f2ce6b --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True, } + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.so'], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' -- GitLab From d4d4527531f2066aa3f45f801f17ae64e45ae2b4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 12:36:47 +0200 Subject: [PATCH 1011/1172] Rename cp2k directory to avoid 'argument list is too long' --- .../c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index c8c01fe2ca..e2d55ed50b 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -20,6 +20,9 @@ patches = [ 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] +# short directory name to avoid 'argument list is too long' +preconfigopts = 'cd .. && mv cp2k-68331* cp2k && cd cp2k && ' + dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.1'), -- GitLab From a75aff8578e878f5f8b75f9feea3a5125feadae4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 12:43:27 +0200 Subject: [PATCH 1012/1172] Revert useless fix --- .../c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index e2d55ed50b..c8c01fe2ca 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -20,9 +20,6 @@ patches = [ 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -# short directory name to avoid 'argument list is too long' -preconfigopts = 'cd .. && mv cp2k-68331* cp2k && cd cp2k && ' - dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.1'), -- GitLab From 47afbf970b1e6c770ebd2a6eaefad9146639b1a0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 13:37:00 +0200 Subject: [PATCH 1013/1172] Another try to avoid long directory name --- .../c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index c8c01fe2ca..6de3d85af3 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -20,6 +20,8 @@ patches = [ 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] +unpack_options = ' && mv cp2k-68331* cp2k' + dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.1'), -- GitLab From d2f3268059555fd6543d5e0f63eb8230833d7b79 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 13:51:24 +0200 Subject: [PATCH 1014/1172] Added clarifying comment to CP2k easyconfig with PLUMED --- .../easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb index 6de3d85af3..1e3ba56c1e 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -20,6 +20,7 @@ patches = [ 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] +# use short directory names to avoid 'argument list is too long' in build process unpack_options = ' && mv cp2k-68331* cp2k' dependencies = [ -- GitLab From 55d8606822017a9cce3eff8583f87124fef19e9c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 15:58:50 +0200 Subject: [PATCH 1015/1172] Use PLUMED with MPI --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb index 3b3039884a..a957863170 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -14,6 +14,7 @@ description = """PLUMED is an open source library for free energy calculations i """ toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'mpi': 'True'} source_urls = ['https://github.com/plumed/plumed2/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 85d74a3c27b856a726e39fd60f4d83bfc8eaada5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 16:02:15 +0200 Subject: [PATCH 1016/1172] Use correct mpi keyword --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb index a957863170..4cccf2ceee 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -14,7 +14,7 @@ description = """PLUMED is an open source library for free energy calculations i """ toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'mpi': 'True'} +toolchainopts = {'usempi': 'True'} source_urls = ['https://github.com/plumed/plumed2/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 16b929b82c72fae68551b23a443eab9802120d2e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 11 Sep 2015 16:34:19 +0200 Subject: [PATCH 1017/1172] Fix plumed to use MPI --- .../p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch | 38 +++++++++++++++++++ .../p/PLUMED/PLUMED-2.1.3-intel-2015a.eb | 2 +- 2 files changed, 39 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch index c96081c3a8..d3cf60fc92 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch @@ -37,3 +37,41 @@ diff -urN plumed-2.0.4.orig/configurations/linux.icc plumed-2.0.4/configurations GCCDEP=g++ +--- plumed-2.0.4.orig/configurations/linux.mpi.icc 2015-06-30 10:02:14.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.mpi.icc 2015-09-11 16:32:00.543631846 +0200 +@@ -1,22 +1,23 @@ + + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++ ++LIBS:=-ldl $(LIBS) ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=mpicc -shared $(CFLAGS) +-LD=mpic++ +-LDF90=mpif90 +-CXX=mpic++ +-CC=mpicc +-FC=mpif90 ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=mpic++ + diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb index 4cccf2ceee..89a5511e51 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -23,7 +23,7 @@ patches = ['PLUMED-2.0.4_eb-env-vars.patch'] skipsteps = ['configure'] -prebuildopts = " ./configure.sh linux.icc && source sourceme.sh && " +prebuildopts = " ./configure.sh linux.mpi.icc && source sourceme.sh && " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " sanity_check_paths = { -- GitLab From 4cfec6a74e048c9921429ee1b0b7725100686dda Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 14 Sep 2015 12:09:05 +0200 Subject: [PATCH 1018/1172] Spark 1.5.0 made available using Java 1.7 since Hadoop eb files use that too. --- easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb | 27 ++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb new file mode 100644 index 0000000000..081d6d615b --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.5.0' + +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/', +] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 90109bbb03cf07db52f62d966c88e5438adeee76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2015 17:01:10 +0200 Subject: [PATCH 1019/1172] {lib}[intel/2015b] phonopy 1.9.6 --- .../f/freetype/freetype-2.5.5-intel-2015b.eb | 21 +++++++++++ .../l/libxslt/libxslt-1.1.28-intel-2015b.eb | 24 ++++++++++++ .../l/libyaml/libyaml-0.1.6-intel-2015b.eb | 28 ++++++++++++++ .../lxml-3.4.4-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++ ...plotlib-1.4.3-intel-2015b-Python-2.7.10.eb | 37 +++++++++++++++++++ .../PyYAML-3.11-intel-2015b-Python-2.7.10.eb | 32 ++++++++++++++++ ...phonopy-1.9.6-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++ 7 files changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb new file mode 100644 index 0000000000..baf0037fb6 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -0,0 +1,21 @@ +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': 'intel', 'version': '2015b'} + +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/libxslt/libxslt-1.1.28-intel-2015b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.eb new file mode 100644 index 0000000000..6524ad39ef --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.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': '2015b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb new file mode 100644 index 0000000000..581b8cb56b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.6' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.so"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..6f981f8afa --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'lxml' +version = '3.4.4' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28'), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..df9c676c65 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +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': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..c99ae13f38 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.11' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % py_short_ver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..3007b29a1b --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.9.6' + +homepage = 'http://phonopy.sourceforge.net/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), + ('lxml', '3.4.4', versionsuffix), + ('PyYAML', '3.11', versionsuffix), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pythonshortversion + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pythonshortversion), pylibdir)], +} + +moduleclass = 'lib' -- GitLab From e915c7b49a651d3304442d4e7887a3982d0290d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2015 17:20:37 +0200 Subject: [PATCH 1020/1172] add missing easyconfig for libpng 1.6.16 --- .../l/libpng/libpng-1.6.16-intel-2015b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb new file mode 100644 index 0000000000..21ff2f7764 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.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': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From a8137680278ba1bb2e7666524f4a83d647c41fde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2015 19:10:27 +0200 Subject: [PATCH 1021/1172] {lib}[intel/2015b] phonopy 1.9.6.2 --- ...onopy-1.9.6.2-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..47381e3887 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.9.6.2' + +homepage = 'http://phonopy.sourceforge.net/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), + ('lxml', '3.4.4', versionsuffix), + ('PyYAML', '3.11', versionsuffix), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pythonshortversion + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pythonshortversion), pylibdir)], +} + +moduleclass = 'lib' -- GitLab From 66dede5c999409656f0aa772ac4b9338b61bda38 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 15 Sep 2015 09:48:27 +0200 Subject: [PATCH 1022/1172] typos corrected, comments considered --- ...-N-3.6.11-intel-2015a.eb => MIGRATE-N-3.6.11-intel-2015a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MIGRATE-N/{MIRGATE-N-3.6.11-intel-2015a.eb => MIGRATE-N-3.6.11-intel-2015a.eb} (96%) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb similarity index 96% rename from easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb rename to easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb index 33a96243d5..9d2b2c9a30 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIRGATE-N-3.6.11-intel-2015a.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -configopts = '--enable-A4 CC=icc ' +configopts = '--enable-A4 "CC=$CC" ' prebuildopts = 'make mpis && make clean && ' start_dir = 'src' -- GitLab From 5ee4425c3356a2e30c6679d88288938f18f2495f Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 13:58:55 +0300 Subject: [PATCH 1023/1172] Minor changes in nvciew config format --- .../n/ncview/ncview-2.1.2-goolf-1.4.10.eb | 39 +++++++++++++++++++ .../n/ncview/ncview-2.1.2-ictce-5.3.0.eb | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..01beb09931 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.2' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib" + +dependencies = [ + ('netCDF-Fortran', '4.2'), + ('UDUNITS', '2.1.24'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..cc28eac2df --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.2' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib" + +dependencies = [ + ('netCDF-Fortran', '4.2'), + ('UDUNITS', '2.1.24'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} -- GitLab From d070d4be0dd11502a0fd357e6258f214888dcb10 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 16 Sep 2015 14:30:27 +0300 Subject: [PATCH 1024/1172] Removing accidentally commited files --- .../cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb | 33 ---------------- .../f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb | 38 ------------------- .../Trim_Galore-0.3.7-goolf-1.4.10.eb | 28 -------------- 3 files changed, 99 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb delete mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb deleted file mode 100644 index 76d2e9cb85..0000000000 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = "PythonPackage" - -name = 'cutadapt' -version = '1.5' - -homepage = 'http://code.google.com/p/cutadapt/' -description = """ cutadapt removes adapter sequences - from high-throughput sequencing data. This is usually - necessary when the read length of the sequencing machine - is longer than the molecule that is sequenced, for - example when sequencing microRNAs. """ - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.3' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = "-%s-%s" % (python, pyver) - -dependencies = [ - (python, pyver), -] - -sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb deleted file mode 100644 index bd99041b10..0000000000 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ /dev/null @@ -1,38 +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 -# License:: MIT/GPL -# -## -easyblock = "PackedBinary" - -name = 'FastQC' -version = '0.10.1' - -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': 'goolf', 'version': '1.4.10'} - -sources = ['%(namelower)s_v%(version)s.zip'] -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] - -java = 'Java' -javaver = '1.7.0_21' - -dependencies = [('Java', '1.7.0_21', '', True)] - -install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" - -sanity_check_paths = { - 'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt", - "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.32.jar"], - 'dirs': ["Contaminants", "Help", "Templates", "uk"], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb deleted file mode 100644 index 425d2e339b..0000000000 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = "PackedBinary" - -name = 'Trim_Galore' -version = '0.3.7' - -homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' -description = """A wrapper tool around Cutadapt and FastQC to consistently apply -quality and adapter trimming to FastQ files, with some extra functionality for -MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -sources = ['%(namelower)s_v%(version)s.zip'] -source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] - -install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" - -dependencies = [ - ('FastQC', '0.10.1'), - ('cutadapt', '1.5', '-Python-2.7.3'), -] - -sanity_check_paths = { - 'files': ["trim_galore"], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From b892ab56bd87009ecab9311916eca0b73b558c62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2015 13:48:38 +0200 Subject: [PATCH 1025/1172] {cae}[intel/2015b] OpenFOAM 2.4.0 --- .../o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb | 38 ++++++ .../o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch | 127 ++++++++++++++++++ .../o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch | 57 ++++++++ 3 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb new file mode 100644 index 0000000000..68a091945c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.4.0' + +homepage = 'http://www.openfoam.com/' +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': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch new file mode 100644 index 0000000000..e84b1107b2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch @@ -0,0 +1,127 @@ +diff -ru OpenFOAM-2.4.0/etc/config/scotch.sh OpenFOAM-2.4.0.patched/etc/config/scotch.sh +--- OpenFOAM-2.4.0/etc/config/scotch.sh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/scotch.sh 2015-09-16 09:53:43.280706774 +0200 +@@ -33,7 +33,11 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++if [ -n "${SCOTCH_ROOT}" ] ; then ++ export SCOTCH_ARCH_PATH="${SCOTCH_ROOT}" ++else ++ export SCOTCH_VERSION=scotch_6.0.3 ++ export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++fi + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-2.4.0/etc/config/settings.csh OpenFOAM-2.4.0.patched/etc/config/settings.csh +--- OpenFOAM-2.4.0/etc/config/settings.csh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/settings.csh 2015-09-16 09:47:42.863934554 +0200 +@@ -339,7 +339,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + switch ("$WM_MPLIB") + case SYSTEMOPENMPI: +diff -ru OpenFOAM-2.4.0/etc/config/settings.sh OpenFOAM-2.4.0.patched/etc/config/settings.sh +--- OpenFOAM-2.4.0/etc/config/settings.sh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/settings.sh 2015-09-16 09:47:42.883935006 +0200 +@@ -359,7 +359,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + case "$WM_MPLIB" in + SYSTEMOPENMPI) +@@ -573,6 +573,11 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++ ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C +--- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-09-16 09:47:42.903935458 +0200 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options 2015-09-16 09:54:52.402822251 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-09-16 09:47:42.903935458 +0200 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-2.4.0.patched/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-2.4.0/src/parallel/decompose/scotchDecomp/Make/options 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/scotchDecomp/Make/options 2015-09-16 09:47:42.903935458 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch new file mode 100644 index 0000000000..58e0c4eaf6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch @@ -0,0 +1,57 @@ +fix lib dir, using an external SCOTCH +author: Kenneth Hoste (kenneth.hoste@ugent.be) +diff -ru ThirdParty-2.4.0.ORIG/Allwmake ThirdParty-2.4.0/Allwmake +--- ThirdParty-2.4.0.ORIG/Allwmake 2014-02-06 16:31:37.000000000 +0100 ++++ ThirdParty-2.4.0/Allwmake 2014-07-08 00:32:02.955084962 +0200 +@@ -110,12 +110,12 @@ + ;; + + MPICH) +- if [ -r $MPI_ARCH_PATH/lib/libmpich.so ] ++ if [ -r $MPI_ARCH_PATH/lib64/libmpich.so ] + then + echo " have $WM_MPLIB shared library ($FOAM_MPI)" + echo + echo +- elif [ -r $MPI_ARCH_PATH/lib/libmpich.a ] ++ elif [ -r $MPI_ARCH_PATH/lib64/libmpich.a ] + then + echo " have $WM_MPLIB static library ($FOAM_MPI)" + echo +@@ -195,6 +195,13 @@ + echo " scotch header in $SCOTCH_ARCH_PATH/include" + echo " scotch libs in $FOAM_EXT_LIBBIN" + echo ++elif [ -f $SCOTCH_ARCH_PATH/include/scotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.a \) ] ++then ++ echo " scotch header in $SCOTCH_ARCH_PATH/include" ++ echo " scotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -256,6 +263,13 @@ + echo " ptscotch header in $SCOTCH_ARCH_PATH/include/$FOAM_MPI" + echo " ptscotch libs in $FOAM_EXT_LIBBIN/$FOAM_MPI" + echo ++ elif [ -f $SCOTCH_ARCH_PATH/include/ptscotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.a \) ] ++ then ++ echo " ptscotch header in $SCOTCH_ARCH_PATH/include" ++ echo " ptscotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -296,7 +310,7 @@ + fi + + # verify existence of scotch include +- [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h ] || { ++ [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h -o -f $SCOTCH_ARCH_PATH/include/ptscotch.h ] || { + echo + echo " WARNING: required include file 'ptscotch.h' not found!" + echo -- GitLab From 9157fbf0724e079aaa90dd2b38aa6162a216b8b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2015 13:52:16 +0200 Subject: [PATCH 1026/1172] add comments in patch file for OpenFOAM 2.4.0 --- easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch index e84b1107b2..6c0f6e24a6 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch @@ -1,3 +1,5 @@ +add support for picking up dependencies (i.e. SCOTCH) provided via EasyBuild +author: Kenneth Hoste (kenneth.hoste@ugent.be) diff -ru OpenFOAM-2.4.0/etc/config/scotch.sh OpenFOAM-2.4.0.patched/etc/config/scotch.sh --- OpenFOAM-2.4.0/etc/config/scotch.sh 2015-05-22 11:50:30.000000000 +0200 +++ OpenFOAM-2.4.0.patched/etc/config/scotch.sh 2015-09-16 09:53:43.280706774 +0200 -- GitLab From 76d3a0d390532db554c078ef5e1fec5b465fbcb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2015 14:54:52 +0200 Subject: [PATCH 1027/1172] {cae}[dummy] ANSYS CFD 16.2 --- .../easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb new file mode 100644 index 0000000000..4d52f97071 --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb @@ -0,0 +1,15 @@ +easyblock = 'FLUENT' + +name = 'ANSYS_CFD' +version = '16.2' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics' +description = """ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, + the impact of fluid flows on your product throughout design and manufacturing as well as during end use. + ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDSTRUCTURES_162_LINX64.tar'] + +moduleclass = 'cae' -- GitLab From bd27b286c42543f62323a80516f997f465d5d94b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 Sep 2015 15:52:38 +0200 Subject: [PATCH 1028/1172] {tools} [foss-2015a] Subversion (REVIEW) --- .../a/APR-util/APR-util-1.5.4-foss-2015a.eb | 29 +++++++++++++++ .../easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb | 19 ++++++++++ .../SCons-2.3.6-foss-2015a-Python-2.7.9.eb | 26 ++++++++++++++ .../s/Serf/Serf-1.3.8-foss-2015a.eb | 35 +++++++++++++++++++ .../s/Serf/Serf-1.3.8_SCons_ld_lib.patch | 15 ++++++++ .../s/Serf/Serf-1.3.8_remve_c99_comment.patch | 15 ++++++++ .../Subversion-1.8.14-foss-2015a.eb | 34 ++++++++++++++++++ 7 files changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb new file mode 100644 index 0000000000..7eb29d9595 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.5.4' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('APR', '1.5.2'), + ('SQLite', '3.8.8.1'), + ('expat', '2.1.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb b/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb new file mode 100644 index 0000000000..fdaff97c8e --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.5.2' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.so", "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..862d3382ac --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb new file mode 100644 index 0000000000..766c8a1db4 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -0,0 +1,35 @@ +name = 'Serf' +version = '1.3.8' + +homepage = 'http://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + ('%(name)s-%(version)s_remve_c99_comment.patch'), + ('%(name)s-%(version)s_SCons_ld_lib.patch'), +] + +builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] + +dependencies = [ + ('APR', '1.5.2'), + ('APR-util', '1.5.4'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch new file mode 100644 index 0000000000..5dbaafe5c9 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch @@ -0,0 +1,15 @@ +#SCons deletes LD_LIBRARY_PATH, and cannot use non-system python in test phase. +#This restores original LD_LIBRARY_PATH +#B. Hajgato 16th September 2015 +--- SConstruct.org 2014-02-04 21:11:10.000000000 +0100 ++++ SConstruct 2015-09-16 14:51:43.245327962 +0200 +@@ -436,7 +436,8 @@ + TEST_EXES = [ os.path.join('test', '%s' % (prog)) for prog in TEST_PROGRAMS ] + + env.AlwaysBuild(env.Alias('check', TEST_EXES, sys.executable + ' build/check.py', +- ENV={'PATH' : os.environ['PATH']})) ++ ENV={'PATH' : os.environ['PATH'], ++ 'LD_LIBRARY_PATH' : os.environ['LD_LIBRARY_PATH']})) + + # Find the (dynamic) library in this directory + tenv.Replace(RPATH=thisdir) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch new file mode 100644 index 0000000000..ec94f9c824 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch @@ -0,0 +1,15 @@ +#Remove C99 style comment (from file in test phase) +#https://code.google.com/p/serf/source/detail?r=2443 +--- test/test_buckets.c.org 2015-09-16 14:22:37.884308890 +0200 ++++ test/test_buckets.c 2015-09-16 14:23:44.311351710 +0200 +@@ -1232,9 +1232,9 @@ + + /* The largest buffer we should need is 0.1% larger than the + uncompressed data, + 12 bytes. This info comes from zlib.h. ++ buf_size = orig_len + (orig_len / 1000) + 12; + Note: This isn't sufficient when using Z_NO_FLUSH and extremely compressed + data. Use a buffer bigger than what we need. */ +-// buf_size = orig_len + (orig_len / 1000) + 12; + buf_size = 100000; + + write_buf = apr_palloc(pool, buf_size); diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000..9bae8b637e --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.8.14' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('APR', '1.5.2'), + ('APR-util', '1.5.4'), + ('SQLite', '3.8.8.1'), + ('zlib', '1.2.8'), + ('Serf', '1.3.8'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 4c67246a1711d84ed4058c73736bfd54f3ae4c4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2015 19:38:28 +0200 Subject: [PATCH 1029/1172] fix name of easyblock to EB_FLUENT --- easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb index 4d52f97071..7497b3bc67 100644 --- a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb @@ -1,4 +1,4 @@ -easyblock = 'FLUENT' +easyblock = 'EB_FLUENT' name = 'ANSYS_CFD' version = '16.2' -- GitLab From 724e660a3822592b8803bdb5d3d76f5dcc2cb6bd Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 17 Sep 2015 12:26:31 +0300 Subject: [PATCH 1030/1172] Minor changes in formatting --- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) 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 334b02c101..d594006934 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 @@ -1,10 +1,12 @@ +easyblock = 'ConfigureMake' + name = 'Tk' version = '8.6.1' 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.""" - +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': 'ictce', 'version': '5.3.0'} -- GitLab From 3f4a237196ca3aa6b47c5290db80037e98406f64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2015 11:33:38 +0200 Subject: [PATCH 1031/1172] add Rsubread in Bioconductor easyconfigs --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 1 + .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index f4e89df8a7..b172ff0137 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -132,6 +132,7 @@ exts_list = [ ('derfinderHelper', '1.2.0', bioconductor_options), ('derfinder', '1.2.1', bioconductor_options), ('polyester', '1.4.0', bioconductor_options), + ('Rsubread', '1.18.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 2c428f8a32..8c43cb0960 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -132,6 +132,7 @@ exts_list = [ ('derfinderHelper', '1.2.0', bioconductor_options), ('derfinder', '1.2.1', bioconductor_options), ('polyester', '1.4.0', bioconductor_options), + ('Rsubread', '1.18.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} -- GitLab From cadff634ee76173b6c78e2a4c0b735cc36628db2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2015 14:45:38 +0200 Subject: [PATCH 1032/1172] {cae}[intel/2015b] ISIS 4.2.1 --- .../i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo | Bin 0 -> 12288 bytes .../i/ISIS/ISIS-4.2.1-intel-2015b.eb | 50 ++++++++++++++++++ .../easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch | 17 ++++++ .../ISIS-4.2.1_specify-system-in-tests.patch | 38 +++++++++++++ .../m/METIS/METIS-4.0.3-intel-2015b.eb | 18 +++++++ 5 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo create mode 100644 easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch create mode 100644 easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch create mode 100644 easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb diff --git a/easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo b/easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo new file mode 100644 index 0000000000000000000000000000000000000000..3954dc5749db90cc1d5b3ddb49afe8ecf0a5ecec GIT binary patch literal 12288 zcmeI2O>Z1E7{?vNr9f!`ap3@FX*8+2JCof_161rGOt)kpZ^~{6qKa0Y8Sk#y+3_&; zj^sTU$GQD}tyO_3V$vir?~^4Uub}HCoHftIX%|L&I|)9RWwc5;#xV zt>&_+zE*pczVQ5>9Ho{;aLZ=qYzr_cw`KGcGm&^hSOX9)QN`Vsm9dJlRR z>OgNn_ns!?5UQX$^dfWzv3&!54SfZfSZ_n_aReLzN5Bzq1RMcJz!7--2ux*KWjx84 zQnW+8gmDkQKoW|_OGT-?YxJfUu5Cm&dS0D+<{GFece)!{q@0Sw;%O7O=`=Xwf=hNQupoM?d`sO5o98!#^ub;BmZfH z*#J9{alaGo?roj=j?fG+@70xHS_pp3lldS!5%N^95<&6|(`XW6FZ0SmD|!XfdeoS` zf9>~Zq5QoshMYsAXGF0`x?8<&hb0LwG)2fZNaX)MU&P)oD^9AsV8}M&7c#eNvC&Yv z6h$ME(?aIB+pIcGcu*5j;8t{DY;Jn98_HG5ZI)+VO@>om@I2*tf)!;9mpq#$W3}Qh z`)%(sjIgw@#%7L8@*9gwhrCn>;IbMB0Qaqh@uy@}CNtCC_TFyT-Pqpm?hg9ze0VVb zHmJ&M=4z~Up{@nN2+M!Oee9y#AC_nasXWRv$mfRX~imi!mbdx1xnpe}9mvoCA3SKsPT23%k{&B@@GW=StM$ldJT)`^_ zs1#h9&8@_=%B&TYLpl`jPFbGPL>8zW2|cC^MapT(@(~6dQdSh1NM@evCaA1RMLwb# zo0=2A#HFh;#;KHRq){bU111dcKpZAbR45u^DwVcgSVnJTl}PFJ6W|hwqDl_+5i2>3 z0XU`TYfrFt&&GCoc2R8E(jGZJjWnE+v7GXPAxtdh2Pd&8czv0yjZ1ZVAEV2}-w literal 0 HcmV?d00001 diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb new file mode 100644 index 0000000000..92c83853da --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'ISIS' +version = '4.2.1' + +homepage = 'https://gforge.irsn.fr/gf/project/isis/' +description = """ISIS is Computational Fluid Dynamics software based on CALIF3S and PELICANS libraries. It is + intensively used for simulation of fires and copes with a wide range of applications, including laminar or turbulent + flows, possibly reactive, governed by incompressible or low Mach number Navier-Stokes equations.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://gforge.irsn.fr/gf/download/frsrelease/3626/39835/'] +sources = [SOURCELOWER_TGZ] + +patches = [ + 'ISIS-%(version)s_impi.patch', + 'ISIS-%(version)s_specify-system-in-tests.patch', +] + +dependencies = [('METIS', '4.0.3')] + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' +buildininstalldir = True + +# options used both in build and test step +commonopts = 'CCC="$CC" ISISHOME=%(installdir)s/ISIS ' +commonopts += 'WITH_MPI=1 MPIRUN=$EBROOTIMPI/bin64/mpiexec ' +commonopts += 'WITH_METIS=1 METISPATH=$EBROOTMETIS/lib ' + +buildopts = "install LICENSE=accept " + commonopts + +parallel = 1 + +runtest = 'test ' + commonopts +runtest += '&& make test_install ' + commonopts +runtest += '&& make test_MPI ' + commonopts +runtest += '&& make test_METIS ' + commonopts + +binaries = ['isis', 'isis_batch', 'isis_run', 'isis_s2c', 'isis_sylvia'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['init.csh', 'init.sh', 'xisis'] + binaries], + 'dirs': ['CALIFS', 'ISIS', 'PELICANS'], +} + +modextrapaths = {'ISISHOME': 'ISIS'} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch new file mode 100644 index 0000000000..ae58465328 --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch @@ -0,0 +1,17 @@ +--- PELICANS/etc/extra-Linux.mak.orig 2015-09-04 11:28:14.263778000 +0200 ++++ PELICANS/etc/extra-Linux.mak 2015-09-04 11:31:37.180400000 +0200 +@@ -152,10 +152,10 @@ + CPPFLAGS += -I$(PELICANSHOME)/$(EXTPACKS)/MPI/include -DMPIRUN=\"$(MPIRUN)\" + endif + +-CPPFLAGS += -I$(MPIPATH)/include +-MPIPATH = $(EXTRA_LIBS_DIR)/openmpi +-LIBPATH += $(MPIPATH)/lib +-LDLIBS += -lmpi -lmpi_cxx ++MPIPATH = $(EBROOTIMPI) ++CPPFLAGS += -I$(MPIPATH)/include64 ++LIBPATH += $(MPIPATH)/lib64 ++LDLIBS += -lmpi -lmpicxx + endif + + diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch new file mode 100644 index 0000000000..9434f2f644 --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch @@ -0,0 +1,38 @@ +--- Makefile.orig 2015-09-17 14:21:50.947592000 +0200 ++++ Makefile 2015-09-17 14:22:33.015119930 +0200 +@@ -134,7 +134,7 @@ + @echo "| Test failed: ExternalAPI MPI not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -no_check_data ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -system Linux-$(CCC) -no_check_data + @ $(RM) resu_MPI + endif + +@@ -147,7 +147,7 @@ + @echo "| Test failed: ExternalAPI MPI not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -no_check_data -opt2 ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -system Linux-$(CCC) -no_check_data -opt2 + @ $(RM) resu_MPI + endif + @ cd $(APPLI_DIR) ; $(MAKE) test_install CCC=$(CCC) OPT_TEST=$(OPT_TEST) +@@ -161,7 +161,7 @@ + @echo "| Test failed: ExternalAPI METIS not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -no_check_data ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -system Linux-$(CCC) -no_check_data + @ $(RM) resu_METIS + endif + +@@ -174,7 +174,7 @@ + @echo "| Test failed: ExternalAPI METIS not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -no_check_data -opt2 ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -system Linux-$(CCC) -no_check_data -opt2 + @ $(RM) resu_METIS + endif + diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb new file mode 100644 index 0000000000..c24b8fd216 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb @@ -0,0 +1,18 @@ +name = 'METIS' +version = '4.0.3' + +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': '2015b'} +toolchainopts = {'optarch': True, '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', +] + +moduleclass = 'math' -- GitLab From ec95cf5516fb2a794c9619990f992e38954ffe35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2015 14:47:37 +0200 Subject: [PATCH 1033/1172] add comments in patches for ISIS --- easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch | 2 ++ .../easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch index ae58465328..2a47d76825 100644 --- a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch @@ -1,3 +1,5 @@ +fix hardcoded MPI-related variables for EB-provided Intel MPI +author: Kenneth Hoste (Ghent University) --- PELICANS/etc/extra-Linux.mak.orig 2015-09-04 11:28:14.263778000 +0200 +++ PELICANS/etc/extra-Linux.mak 2015-09-04 11:31:37.180400000 +0200 @@ -152,10 +152,10 @@ diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch index 9434f2f644..fdce1c97aa 100644 --- a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch @@ -1,3 +1,5 @@ +specify -system flag to fix path to binaries used by tests +author: Kenneth Hoste (Ghent University) --- Makefile.orig 2015-09-17 14:21:50.947592000 +0200 +++ Makefile 2015-09-17 14:22:33.015119930 +0200 @@ -134,7 +134,7 @@ -- GitLab From 832d61aace7dc0abc9a3d6d1bf4d590007866039 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2015 21:11:33 +0200 Subject: [PATCH 1034/1172] fix MPIRUN build/test option --- easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb index 92c83853da..eea668f44a 100644 --- a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb @@ -27,7 +27,7 @@ buildininstalldir = True # options used both in build and test step commonopts = 'CCC="$CC" ISISHOME=%(installdir)s/ISIS ' -commonopts += 'WITH_MPI=1 MPIRUN=$EBROOTIMPI/bin64/mpiexec ' +commonopts += 'WITH_MPI=1 MPIRUN=$EBROOTIMPI/bin64/mpiexec.hydra ' commonopts += 'WITH_METIS=1 METISPATH=$EBROOTMETIS/lib ' buildopts = "install LICENSE=accept " + commonopts -- GitLab From 12858dc560c6be284b8138a3ff94465c3210b0ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2015 21:27:36 +0200 Subject: [PATCH 1035/1172] remove .swo file --- .../i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo | Bin 12288 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo diff --git a/easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo b/easybuild/easyconfigs/i/ISIS/.ISIS-4.2.1-intel-2015a.eb.swo deleted file mode 100644 index 3954dc5749db90cc1d5b3ddb49afe8ecf0a5ecec..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI2O>Z1E7{?vNr9f!`ap3@FX*8+2JCof_161rGOt)kpZ^~{6qKa0Y8Sk#y+3_&; zj^sTU$GQD}tyO_3V$vir?~^4Uub}HCoHftIX%|L&I|)9RWwc5;#xV zt>&_+zE*pczVQ5>9Ho{;aLZ=qYzr_cw`KGcGm&^hSOX9)QN`Vsm9dJlRR z>OgNn_ns!?5UQX$^dfWzv3&!54SfZfSZ_n_aReLzN5Bzq1RMcJz!7--2ux*KWjx84 zQnW+8gmDkQKoW|_OGT-?YxJfUu5Cm&dS0D+<{GFece)!{q@0Sw;%O7O=`=Xwf=hNQupoM?d`sO5o98!#^ub;BmZfH z*#J9{alaGo?roj=j?fG+@70xHS_pp3lldS!5%N^95<&6|(`XW6FZ0SmD|!XfdeoS` zf9>~Zq5QoshMYsAXGF0`x?8<&hb0LwG)2fZNaX)MU&P)oD^9AsV8}M&7c#eNvC&Yv z6h$ME(?aIB+pIcGcu*5j;8t{DY;Jn98_HG5ZI)+VO@>om@I2*tf)!;9mpq#$W3}Qh z`)%(sjIgw@#%7L8@*9gwhrCn>;IbMB0Qaqh@uy@}CNtCC_TFyT-Pqpm?hg9ze0VVb zHmJ&M=4z~Up{@nN2+M!Oee9y#AC_nasXWRv$mfRX~imi!mbdx1xnpe}9mvoCA3SKsPT23%k{&B@@GW=StM$ldJT)`^_ zs1#h9&8@_=%B&TYLpl`jPFbGPL>8zW2|cC^MapT(@(~6dQdSh1NM@evCaA1RMLwb# zo0=2A#HFh;#;KHRq){bU111dcKpZAbR45u^DwVcgSVnJTl}PFJ6W|hwqDl_+5i2>3 z0XU`TYfrFt&&GCoc2R8E(jGZJjWnE+v7GXPAxtdh2Pd&8czv0yjZ1ZVAEV2}-w -- GitLab From e17e43b586a1779373a8f226ae6111bab8c8baf4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Sep 2015 09:06:59 +0200 Subject: [PATCH 1036/1172] don't patch symlink --- .../o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch | 22 ------------------- 1 file changed, 22 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch index 6c0f6e24a6..879e7e0b73 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch @@ -53,28 +53,6 @@ diff -ru OpenFOAM-2.4.0/etc/config/settings.sh OpenFOAM-2.4.0.patched/etc/config *) export FOAM_MPI=dummy ;; -diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C ---- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-05-22 11:50:30.000000000 +0200 -+++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-09-16 09:47:42.903935458 +0200 -@@ -112,6 +112,8 @@ - - \*---------------------------------------------------------------------------*/ - -+#include "mpi.h" -+ - #include "ptscotchDecomp.H" - #include "addToRunTimeSelectionTable.H" - #include "Time.H" -@@ -121,8 +123,8 @@ - - extern "C" - { --#include - #include "mpi.h" -+#include - #include "ptscotch.h" - } - diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options --- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options 2015-05-22 11:50:30.000000000 +0200 +++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options 2015-09-16 09:54:52.402822251 +0200 -- GitLab From 49f6030c48ee6cfd07da3bcd71404b837844a1d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Sep 2015 09:13:47 +0200 Subject: [PATCH 1037/1172] set optarch toolchain option to False for ISIS --- easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb index eea668f44a..2a084a9882 100644 --- a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb @@ -9,6 +9,8 @@ description = """ISIS is Computational Fluid Dynamics software based on CALIF3S flows, possibly reactive, governed by incompressible or low Mach number Navier-Stokes equations.""" toolchain = {'name': 'intel', 'version': '2015b'} +# disable optimizing for host architecture, may cause tests to fail due to issues with result validation +toolchainopts = {'optarch': False} source_urls = ['https://gforge.irsn.fr/gf/download/frsrelease/3626/39835/'] sources = [SOURCELOWER_TGZ] -- GitLab From 198ff77e4a8c4b072bde05a8b5b7b914e2c45dfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 10:39:12 +0200 Subject: [PATCH 1038/1172] {data,vis}[intel/2015b] scikit-image 0.11.3, scikit-learn 0.16.1, Pillow 2.9.0 --- .../Pillow-2.9.0-intel-2015b-Python-2.7.10.eb | 23 +++++++++++++ ...-image-0.11.3-intel-2015b-Python-2.7.10.eb | 33 ++++++++++++++++++ ...-learn-0.16.1-intel-2015b-Python-2.7.10.eb | 34 +++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..c3113a6683 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.9.0' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..efa2645234 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.11.3' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), +] + +options = {'modulename': 'skimage'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/skimage' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..d7c757bc82 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} + +moduleclass = 'data' -- GitLab From c88816d4e9597383a1d7a92f8bcb6144889a41d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 11:05:20 +0200 Subject: [PATCH 1039/1172] add Qhull as dependency for sckit-image --- .../c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb | 22 ++++++++++++ .../n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb | 36 +++++++++++++++++++ .../q/Qhull/Qhull-2012.1-intel-2015b.eb | 31 ++++++++++++++++ ...-image-0.11.3-intel-2015b-Python-2.7.10.eb | 1 + 4 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..966a727842 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +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': 'GNU', 'version': '4.9.3-2.25'} + +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' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..82fd4d66d0 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} +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/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb new file mode 100644 index 0000000000..d3f77e6bf5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2012.1' + +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': 'intel', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = ['Qhull-2012.1-intel-fix.patch'] + +builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.so'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb index efa2645234..b7db4d8a25 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb @@ -20,6 +20,7 @@ pyver = '2.7.10' versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ (python, pyver), + ('Qhull', '2012.1'), ] options = {'modulename': 'skimage'} -- GitLab From 7cdc00c2a34f293e8eeebde7778f423a537602c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 11:08:17 +0200 Subject: [PATCH 1040/1172] fix toolchain for CMake build dep in Qhull easyconfig --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index d3f77e6bf5..0f06f3942a 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = ['Qhull-2012.1-intel-fix.patch'] -builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] +builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] sanity_check_paths = { 'files': ['bin/qhull', 'lib/libqhull.so'], -- GitLab From 44b82c8efe79bcc06025f321928ac584be74d6fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 13:23:30 +0200 Subject: [PATCH 1041/1172] add matplotlib/networkx/Pillow as dep for scikit-image --- .../scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb index b7db4d8a25..cb313162b0 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb @@ -21,6 +21,9 @@ versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ (python, pyver), ('Qhull', '2012.1'), + ('matplotlib', '1.4.3', versionsuffix), + ('networkx', '1.10', versionsuffix), + ('Pillow', '2.9.0', versionsuffix), ] options = {'modulename': 'skimage'} -- GitLab From 5b55cd23208b53637326923af49c7790bfe20375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 13:37:52 +0200 Subject: [PATCH 1042/1172] use Qhull_pkgconfig.patch in intel/2015b Qhull easyconfig --- .../easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index 0f06f3942a..568f30abd9 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -15,12 +15,20 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + ('Qhull_pkgconfig.patch', 1), +] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] +postinstallcmds = [ + "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", + "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", +] + sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } -- GitLab From 3deaea36d0469230cbd03dfb26937019456d8795 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 13:39:37 +0200 Subject: [PATCH 1043/1172] add patch to install qhull.pc (pkgconfig) file --- .../q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 14 +++++++++++--- .../q/Qhull/Qhull-2012.1-intel-2014b.eb | 14 +++++++++++--- .../q/Qhull/Qhull-2012.1-intel-2015a.eb | 14 +++++++++++--- .../easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 18 ++++++++++++++++++ 4 files changed, 51 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index dd5a337d1f..664217ffd0 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -15,12 +15,20 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + ('Qhull_pkgconfig.patch', 1), +] -builddependencies = [('CMake', '2.8.12')] +builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] + +postinstallcmds = [ + "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", + "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", +] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 188d2a929c..d99d2d3c01 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -15,12 +15,20 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + ('Qhull_pkgconfig.patch', 1), +] -builddependencies = [('CMake', '2.8.12')] +builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] + +postinstallcmds = [ + "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", + "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", +] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index d32af2c654..5f9bea7b1f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -15,12 +15,20 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + ('Qhull_pkgconfig.patch', 1), +] -builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] +builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] + +postinstallcmds = [ + "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", + "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", +] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch new file mode 100644 index 0000000000..4755ae5de8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -0,0 +1,18 @@ +inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraproject.org/qhull +requires injecting correct values INSTALLDIR and VERSION +author: Kenneth Hoste (UGent) +diff -Naur qhull-2003.1.orig/qhull.pc.in qhull-2003.1/qhull.pc.in +--- qhull-2003.1.orig/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ qhull-2003.1/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 +@@ -0,0 +1,11 @@ ++prefix=INSTALLDIR ++exec_prefix=${prefix} ++includedir=${prefix}/include ++libdir=${prefix}/lib ++ ++Name: qhull ++Description: General dimension convex hull library ++Version: VERSION ++Requires: ++Libs: -L${libdir} -lqhull -lm ++Cflags: -I${includedir} -- GitLab From 5b036fba19de5f1e8fbb9c8a550d3525d80cbcbc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 13:41:14 +0200 Subject: [PATCH 1044/1172] adjust patch level for Qhull_pkgconfig.patch --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 664217ffd0..9f97f355a6 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 1), + ('Qhull_pkgconfig.patch', 0), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index d99d2d3c01..6ead02d06d 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 1), + ('Qhull_pkgconfig.patch', 0), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index 5f9bea7b1f..c602d3fcd2 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 1), + ('Qhull_pkgconfig.patch', 0), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 4755ae5de8..be33649182 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -2,8 +2,8 @@ inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraprojec requires injecting correct values INSTALLDIR and VERSION author: Kenneth Hoste (UGent) diff -Naur qhull-2003.1.orig/qhull.pc.in qhull-2003.1/qhull.pc.in ---- qhull-2003.1.orig/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -+++ qhull-2003.1/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 +--- qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 @@ -0,0 +1,11 @@ +prefix=INSTALLDIR +exec_prefix=${prefix} -- GitLab From 287b5940328e159b20b068effe847069281613b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 13:41:35 +0200 Subject: [PATCH 1045/1172] adjust patch level for Qhull_pkgconfig.patch --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index 568f30abd9..7dd5c4bb66 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 1), + ('Qhull_pkgconfig.patch', 0), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] -- GitLab From 44db947ce078338d8ae1a295ee203971cf75f6a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:00:17 +0200 Subject: [PATCH 1046/1172] fix sanity check in scikit-image easyconfig --- .../scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb index cb313162b0..42f9a9c3ff 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb @@ -29,9 +29,10 @@ dependencies = [ options = {'modulename': 'skimage'} pyshortver = '.'.join(pyver.split('.')[:-1]) +pylibdir = 'lib/python%s/site-packages' % pyshortver sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/skimage' % pyshortver], + 'dirs': ['%s/scikit_image-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver)], } moduleclass = 'vis' -- GitLab From 93e23ad1164b2f0f23ede5483bbefc711e7aebcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:01:34 +0200 Subject: [PATCH 1047/1172] dance around bug w.r.t. patch level zero --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 9f97f355a6..664217ffd0 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 0), + ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 6ead02d06d..d99d2d3c01 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 0), + ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index c602d3fcd2..5f9bea7b1f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 0), + ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index be33649182..c1b61ec650 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -2,8 +2,8 @@ inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraprojec requires injecting correct values INSTALLDIR and VERSION author: Kenneth Hoste (UGent) diff -Naur qhull-2003.1.orig/qhull.pc.in qhull-2003.1/qhull.pc.in ---- qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -+++ qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 +--- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ qhull/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 @@ -0,0 +1,11 @@ +prefix=INSTALLDIR +exec_prefix=${prefix} -- GitLab From b5c5187b0ed1fab11f078ee559e48dce1b2ee5c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:02:09 +0200 Subject: [PATCH 1048/1172] fix patch level specified in Qhull easyconfig --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index 7dd5c4bb66..568f30abd9 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -17,7 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 0), + ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] -- GitLab From a7d9d6f2fcaf9bcbbbf7262670db040c839bc8a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:08:58 +0200 Subject: [PATCH 1049/1172] revert change to Qhull build deps --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 664217ffd0..3bd1d0be7b 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -20,7 +20,7 @@ patches = [ ('Qhull_pkgconfig.patch', 1), ] -builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] +builddependencies = [('CMake', '2.8.12')] postinstallcmds = [ "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index d99d2d3c01..2468cb6e6e 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -20,7 +20,7 @@ patches = [ ('Qhull_pkgconfig.patch', 1), ] -builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] +builddependencies = [('CMake', '2.8.12')] postinstallcmds = [ "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index 5f9bea7b1f..3bfed74936 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -20,7 +20,7 @@ patches = [ ('Qhull_pkgconfig.patch', 1), ] -builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] +builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] postinstallcmds = [ "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", -- GitLab From 4f5862fe5eb6272d98207a0a5718d9fcfd6ba8c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:21:23 +0200 Subject: [PATCH 1050/1172] fix remarks w.r.t. sed command in Qhull's postinstallcmds --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 4 ++-- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 4 ++-- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 2468cb6e6e..eaac48caed 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -23,8 +23,8 @@ patches = [ builddependencies = [('CMake', '2.8.12')] postinstallcmds = [ - "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", - "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", + "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", + "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index 3bfed74936..040192d0da 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -23,8 +23,8 @@ patches = [ builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] postinstallcmds = [ - "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", - "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", + "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", + "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index c1b61ec650..72f9fb0d2f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -1,9 +1,9 @@ inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraproject.org/qhull requires injecting correct values INSTALLDIR and VERSION author: Kenneth Hoste (UGent) -diff -Naur qhull-2003.1.orig/qhull.pc.in qhull-2003.1/qhull.pc.in ---- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -+++ qhull/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 +diff -Naur qhull/qhull.pc qhull/qhull.pc +--- qhull/qhull.pc 1970-01-01 01:00:00.000000000 +0100 ++++ qhull/qhull.pc 2012-07-08 08:04:07.795336862 +0200 @@ -0,0 +1,11 @@ +prefix=INSTALLDIR +exec_prefix=${prefix} -- GitLab From 25c8c6663875969bac38f505418d55e1ce93b588 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:22:20 +0200 Subject: [PATCH 1051/1172] really fix remarks w.r.t. sed command in Qhull's postinstallcmds --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 3bd1d0be7b..88fea3b0f3 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -23,8 +23,8 @@ patches = [ builddependencies = [('CMake', '2.8.12')] postinstallcmds = [ - "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", - "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", + "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", + "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", ] sanity_check_paths = { -- GitLab From 15cc59db978deae53e6724fc27bf88e2f6ca6e26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 14:22:34 +0200 Subject: [PATCH 1052/1172] fix remarks w.r.t. sed command in Qhull's postinstallcmds --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index 568f30abd9..d812a604fb 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -23,8 +23,8 @@ patches = [ builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] postinstallcmds = [ - "cat qhull.pc.in | sed 's@INSTALLDIR@%(installdir)s@g' | sed 's@VERSION@%(version)s@g' > %(builddir)s/qhull.pc", - "install -m644 -D %(builddir)s/qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", + "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", + "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", ] sanity_check_paths = { -- GitLab From db0e41cda51d98d8d29cb5cc8e7c6a18e0d221ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 16:03:31 +0200 Subject: [PATCH 1053/1172] install qhull.pc via CMake rather than using postinstallcmds --- .../easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 6 +----- .../easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 6 +----- .../easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 6 +----- .../q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch | 12 ++++++++++++ easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 12 ++++++------ 5 files changed, 21 insertions(+), 21 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 88fea3b0f3..ba41378b3d 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -17,16 +17,12 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', + 'Qhull-2012.1_CMakeLists-qhull.pc.patch', ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '2.8.12')] -postinstallcmds = [ - "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", - "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", -] - sanity_check_paths = { 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index eaac48caed..70d63e8cf5 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -17,16 +17,12 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', + 'Qhull-2012.1_CMakeLists-qhull.pc.patch', ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '2.8.12')] -postinstallcmds = [ - "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", - "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", -] - sanity_check_paths = { 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index 040192d0da..90c633cad1 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -17,16 +17,12 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', + 'Qhull-2012.1_CMakeLists-qhull.pc.patch', ('Qhull_pkgconfig.patch', 1), ] builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] -postinstallcmds = [ - "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", - "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", -] - sanity_check_paths = { 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch new file mode 100644 index 0000000000..888563307c --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch @@ -0,0 +1,12 @@ +--- CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 ++++ CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 +@@ -430,3 +430,9 @@ + install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) + install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) + install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) ++ ++CONFIGURE_FILE( ++ "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" ++ "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++) ++INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 72f9fb0d2f..1fb9e87788 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -1,18 +1,18 @@ inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraproject.org/qhull -requires injecting correct values INSTALLDIR and VERSION +requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' author: Kenneth Hoste (UGent) -diff -Naur qhull/qhull.pc qhull/qhull.pc ---- qhull/qhull.pc 1970-01-01 01:00:00.000000000 +0100 -+++ qhull/qhull.pc 2012-07-08 08:04:07.795336862 +0200 +diff -Naur qhull/qhull.pc.in qhull/qhull.pc.in +--- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ qhull/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 @@ -0,0 +1,11 @@ -+prefix=INSTALLDIR ++prefix=@CMAKE_INSTALL_PREFIX@ +exec_prefix=${prefix} +includedir=${prefix}/include +libdir=${prefix}/lib + +Name: qhull +Description: General dimension convex hull library -+Version: VERSION ++Version: @qhull_VERSION2@ +Requires: +Libs: -L${libdir} -lqhull -lm +Cflags: -I${includedir} -- GitLab From 622ca633351e586c040892b4edf3e72c6f7b500e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 16:07:42 +0200 Subject: [PATCH 1054/1172] collapse two patches into one --- .../easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 3 +-- .../easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb | 3 +-- .../easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb | 3 +-- .../q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch | 12 ------------ easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 13 ++++++++++++- 5 files changed, 15 insertions(+), 19 deletions(-) delete mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index ba41378b3d..625317ad02 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -17,8 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - 'Qhull-2012.1_CMakeLists-qhull.pc.patch', - ('Qhull_pkgconfig.patch', 1), + 'Qhull_pkgconfig.patch', ] builddependencies = [('CMake', '2.8.12')] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 70d63e8cf5..617a67c44d 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -17,8 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - 'Qhull-2012.1_CMakeLists-qhull.pc.patch', - ('Qhull_pkgconfig.patch', 1), + 'Qhull_pkgconfig.patch', ] builddependencies = [('CMake', '2.8.12')] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index 90c633cad1..1488f628fe 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -17,8 +17,7 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - 'Qhull-2012.1_CMakeLists-qhull.pc.patch', - ('Qhull_pkgconfig.patch', 1), + 'Qhull_pkgconfig.patch', ] builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch deleted file mode 100644 index 888563307c..0000000000 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1_CMakeLists-qhull.pc.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 -+++ CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 -@@ -430,3 +430,9 @@ - install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) - install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) - install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) -+ -+CONFIGURE_FILE( -+ "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" -+ "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" -+) -+INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 1fb9e87788..53f43a015d 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -1,7 +1,18 @@ inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraproject.org/qhull requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' author: Kenneth Hoste (UGent) -diff -Naur qhull/qhull.pc.in qhull/qhull.pc.in +--- qhull/CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 ++++ qhull/CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 +@@ -430,3 +430,9 @@ + install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) + install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) + install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) ++ ++CONFIGURE_FILE( ++ "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" ++ "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++) ++INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) --- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 +++ qhull/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 @@ -0,0 +1,11 @@ -- GitLab From fe44e69aa01f5d4e9bc1cc2039899f29fe08db81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 16:12:07 +0200 Subject: [PATCH 1055/1172] install qhull.pc via CMake rather than using postinstallcmds --- easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb index d812a604fb..8544695ac4 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -17,16 +17,11 @@ source_urls = ['http://www.qhull.org/download/'] patches = [ 'Qhull-2012.1-intel-fix.patch', - ('Qhull_pkgconfig.patch', 1), + 'Qhull_pkgconfig.patch', ] builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] -postinstallcmds = [ - "sed --in-place=bk 's@INSTALLDIR@%(installdir)s@g;s@VERSION@%(version)s@g' qhull.pc", - "install -m644 -D qhull.pc %(installdir)s/lib/pkgconfig/qhull.pc", -] - sanity_check_paths = { 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], -- GitLab From f501ca237f63bdccee91be12c70f52afc79f8987 Mon Sep 17 00:00:00 2001 From: molden Date: Mon, 21 Sep 2015 16:22:19 +0200 Subject: [PATCH 1056/1172] add HBase/1.0.2 --- easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb | 25 ++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb new file mode 100644 index 0000000000..8c6a7116f3 --- /dev/null +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -0,0 +1,25 @@ +easyblock = 'PackedBinary' + +name = 'HBase' +version = '1.0.2' + +homepage = 'http://hbase.apache.org/' +description = """Apache HBase. is the Hadoop database, a distributed, scalable, big data store. """ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin.tar.gz'] +source_urls = ['http://www.us.apache.org/dist/hbase/hbase-1.0.2/'] + +dependencies = [('Java', '1.7.0_80')] + +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/hbase"], + 'dirs': ["bin","conf","docs","hbase-webapps","lib"] +} + +modextravars = {'HBASE_HOME': '%(installdir)s'} + +moduleclass = 'tools' -- GitLab From 5a3f348cd4c32a70b91242d2bfc6c1be350970bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2015 17:10:24 +0200 Subject: [PATCH 1057/1172] add missing easyconfig file --- ...networkx-1.10-intel-2015b-Python-2.7.10.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..3968711a0e --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'tools' -- GitLab From 0ef31d0b33a0ceb3391df54593d98add7b16fde8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 21 Sep 2015 18:52:49 +0200 Subject: [PATCH 1058/1172] Added Python 2.7.10-GNU-4.9.3-2.25-bare for Clang 3.7.0 --- .../b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb | 15 ++++++++ .../libreadline-6.3-GNU-4.9.3-2.25.eb | 29 ++++++++++++++ .../n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 36 ++++++++++++++++++ .../Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 31 +++++++++++++++ .../SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb | 38 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb | 25 ++++++++++++ .../t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb | 24 ++++++++++++ 7 files changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..ee1013b662 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..cdddedcca0 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -0,0 +1,29 @@ +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': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '6.0')] + +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-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..6d3c40aa1f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +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': 'GNU', 'version': '4.9.3-2.25'} +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/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb new file mode 100644 index 0000000000..6c283693fb --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.10' +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': 'GNU', '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', '', ('GCC', '4.9.3-binutils-2.25')), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-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')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..87526d7754 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GNU', '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' + ''.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'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..9f6e6c6b27 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8', '', ('GCC', '4.9.3-binutils-2.25')), +] + +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-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 new file mode 100644 index 0000000000..e5657f531c --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -0,0 +1,24 @@ +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': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From af27e626f86741d8b64c79aa1f4facfce778f3b4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 21 Sep 2015 18:55:11 +0200 Subject: [PATCH 1059/1172] Remove unneeded patch for ncurses 6.0 I think unneeded by now? --- easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 6d3c40aa1f..6d33835f96 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -14,8 +14,6 @@ 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', -- GitLab From ba02218c9b4b523788bb8a87826bd7165434d39a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 21 Sep 2015 20:28:17 +0200 Subject: [PATCH 1060/1172] ncurses 6: update sanity check --- easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 6d33835f96..4012f0e69b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -23,7 +23,7 @@ configopts = [ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + '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']] + -- GitLab From af2c193416088c8226c5d8b2e1a817d74523d5be Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 12:55:04 +0300 Subject: [PATCH 1061/1172] Changes according to comments --- .../c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb index 76d2e9cb85..8e35469e5b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb @@ -13,7 +13,7 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.3' @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'files': ['lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } -- GitLab From 9ac2f28749c2896bb023ebfcb23d616b6a7e8d0e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 22 Sep 2015 16:37:51 +0300 Subject: [PATCH 1062/1172] Minor changes in configopts --- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 d594006934..dc682240ed 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 @@ -15,7 +15,7 @@ sources = ['%s%s-src.tar.gz' % (name.lower(), version)] dependencies = [('Tcl', version)] -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib' start_dir = 'unix' -- GitLab From 0040c268a81697fef7986eee85bb70d903a8f436 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 20:07:25 +0200 Subject: [PATCH 1063/1172] add missing 'easyblock' line --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 6d47d1483d..d58c0d1657 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -1,5 +1,7 @@ -name = "ANTLR" -version = "2.7.7" +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' homepage = "http://www.antlr2.org" description = """ANother Tool for Language Recognition""" @@ -17,7 +19,7 @@ dependencies = [('Java', '1.7.0_60', '', True)] sanity_check_paths = { 'files': ['bin/antlr'], - 'dirs': ["."] + 'dirs': [], } moduleclass = 'lang' -- GitLab From bfbdb238d54d112e0f0ea16bda5bd9cc0a6511f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2015 20:11:07 +0200 Subject: [PATCH 1064/1172] add more missing easyblock lines --- easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb | 5 ++++- .../easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb | 2 ++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb index c79a55883a..434cce1376 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -1,5 +1,8 @@ -name = "NCO" +easyblock = 'ConfigureMake' + +name = 'NCO' version = '4.4.4' + homepage = "http://nco.sourceforge.net" description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb index 161a232d35..e9bf8e9075 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html ## +easyblock = 'ConfigureMake' + name = 'UDUNITS' version = '2.1.24' -- GitLab From 9a310dc5ffef9f2c335f531a35d7f75bf6ac4e9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 07:38:39 +0200 Subject: [PATCH 1065/1172] add missing patch file for ANTLR --- .../easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch new file mode 100644 index 0000000000..e10f61e6d6 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch @@ -0,0 +1,11 @@ +--- antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2006-11-02 10:37:17.000000000 +1300 ++++ antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2014-08-25 13:06:46.541050000 +1200 +@@ -10,6 +10,8 @@ + + #include + ++#include ++#include + #include + + #ifdef HAS_NOT_CCTYPE_H -- GitLab From 468d6d860430c0a7ab0356b4a791f55452c30961 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 07:51:12 +0200 Subject: [PATCH 1066/1172] add missing 'easyblock' lines, fix style issues --- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 12 +++++++----- .../easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb | 2 ++ .../easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb | 1 + easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 7 +++++-- easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb | 2 ++ .../u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb | 6 ++++-- .../easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb | 2 ++ .../easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb | 4 ++-- 8 files changed, 25 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index c65bc28385..3f6e01e0b7 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -1,5 +1,7 @@ -name = "ANTLR" -version = "2.7.7" +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' homepage = "http://www.antlr2.org" description = """ANother Tool for Language Recognition""" @@ -11,13 +13,13 @@ source_urls = ['http://www.antlr2.org/download'] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -configopts = "--disable-examples --disable-csharp" - dependencies = [('Java', '1.7.0_60', '', True)] +configopts = "--disable-examples --disable-csharp" + sanity_check_paths = { 'files': ['bin/antlr'], - 'dirs': ["."] + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb index 155ffc59c6..1fffb8736f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Bison' version = '2.7' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb index baf28602a2..817d701d15 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb @@ -6,6 +6,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb index c9311e3b3b..7d14c8a252 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -1,5 +1,8 @@ -name = "NCO" +easyblock = 'ConfigureMake' + +name = 'NCO' version = '4.4.4' + homepage = "http://nco.sourceforge.net" description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" @@ -18,7 +21,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/ncap'], - 'dirs': ["."] + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb index 43f9f7b55c..43e89506aa 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Szip' version = '2.1' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb index c235471294..e3a2a31a19 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html ## +easyblock = 'ConfigureMake' + name = 'UDUNITS' version = '2.1.24' @@ -23,6 +25,8 @@ toolchainopts = {'opt': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +parallel = 1 + sanity_check_paths = { 'files': [ 'bin/udunits2', @@ -35,6 +39,4 @@ sanity_check_paths = { 'dirs': ['share'], } -parallel = 1 - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb index 6252bc5bba..b5a3851823 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'zlib' version = '1.2.7' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb index 931cdbbadb..25bf52883b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'zlib' version = '1.2.8' @@ -12,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From f0af15b7994dd7f1298c0c677b671c18edad1688 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 07:55:35 +0200 Subject: [PATCH 1067/1172] minor style fix --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index d58c0d1657..1792b55d05 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,10 +13,10 @@ source_urls = ['http://www.antlr2.org/download'] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -configopts = "--disable-examples --disable-csharp" - dependencies = [('Java', '1.7.0_60', '', True)] +configopts = "--disable-examples --disable-csharp" + sanity_check_paths = { 'files': ['bin/antlr'], 'dirs': [], -- GitLab From 6ce80a4835e7e9f92a98399431562dafeb1ad8da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 08:51:03 +0200 Subject: [PATCH 1068/1172] {lang}[intel/2015b] Perl 5.20.3 + exts --- .../p/Perl/Perl-5.20.3-intel-2015b.eb | 909 ++++++++++++++++++ 1 file changed, 909 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb new file mode 100644 index 0000000000..56467d99bf --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.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': '2015b'} +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::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'], + }), + # fails: tests (see https://github.com/exodist/Meta-Builder/issues/2) + #('Meta::Builder', '0.003', { + # 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + #}), + # requires Meta::Builder + #('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'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('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'], + }), + ('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'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('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'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('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'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('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'], + }), + # requires Exporter::Declare + #('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'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + # requires Mock::Quick + #('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 6c73b671e7eacae506276dd7861434fdef1e0fee Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 10:09:44 +0300 Subject: [PATCH 1069/1172] A minor change in sources --- easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 dc682240ed..a79397a5f8 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 @@ -11,7 +11,7 @@ interface (GUI) in many different programming languages.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] -- GitLab From 2113315e614e885af56dcb3f4d349ee14762850d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 09:12:10 +0200 Subject: [PATCH 1070/1172] add missing 'easyblock' line --- easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb index 817d701d15..4ed019fad2 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'expat' version = '2.1.0' -- GitLab From 0bd2fec711a47b37f84f327be2167898f049d13e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 09:33:17 +0200 Subject: [PATCH 1071/1172] add missing M4 easyconfig --- .../easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb 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 new file mode 100644 index 0000000000..3b4187acd1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.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': 'ictce', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c099a10d0d44dc124819c19962e9619f9519da40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 09:35:59 +0200 Subject: [PATCH 1072/1172] reenable commented out extensions after fixing order --- .../p/Perl/Perl-5.20.3-intel-2015b.eb | 52 +++++++++---------- 1 file changed, 24 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb index 56467d99bf..0a30a9f307 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb @@ -191,6 +191,10 @@ exts_list = [ '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'], @@ -291,16 +295,18 @@ exts_list = [ 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], }), - # fails: tests (see https://github.com/exodist/Meta-Builder/issues/2) - #('Meta::Builder', '0.003', { - # 'source_tmpl': 'Meta-Builder-0.003.tar.gz', - # 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - #}), - # requires Meta::Builder - #('Exporter::Declare', '0.114', { - # 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', - # 'source_urls': ['https://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'], @@ -313,10 +319,6 @@ exts_list = [ 'source_tmpl': 'Log-Message-0.08.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), - ('Sub::Uplevel', '0.25', { - 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], - }), ('Mouse', 'v2.4.5', { 'source_tmpl': 'Mouse-v2.4.5.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], @@ -365,10 +367,6 @@ exts_list = [ 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], }), - ('XML::NamespaceSupport', '1.11', { - 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', - 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], - }), ('Test::ClassAPI', '1.06', { 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], @@ -662,11 +660,10 @@ exts_list = [ 'source_tmpl': 'Error-0.17024.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], }), - # requires Exporter::Declare - #('Mock::Quick', '1.110', { - # 'source_tmpl': 'Mock-Quick-1.110.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - #}), + ('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'], @@ -739,11 +736,10 @@ exts_list = [ 'source_tmpl': 'MRO-Compat-0.12.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], }), - # requires Mock::Quick - #('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'], - #}), + ('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'], -- GitLab From 59b132854785c5a4758f960c2cb4f8f84e7d8ae6 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 10:38:41 +0300 Subject: [PATCH 1073/1172] Adding moduleclass --- easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb index cc28eac2df..26ed84e0ca 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb @@ -35,3 +35,5 @@ sanity_check_paths = { 'files': ['bin/ncview'], 'dirs': [], } + +moduleclass = 'vis' -- GitLab From c31551b23506ce26b3094f8d26390d1a6915a3be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 09:40:01 +0200 Subject: [PATCH 1074/1172] bump to 3.7.0 + bump dep versions --- ...-3.6.0-intel-2015a.eb => LLVM-3.7.0-intel-2015a.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/LLVM/{LLVM-3.6.0-intel-2015a.eb => LLVM-3.7.0-intel-2015a.eb} (89%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb similarity index 89% rename from easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb rename to easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb index 86d25e869b..622b77ee48 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb @@ -1,7 +1,7 @@ -easyblock='CMakeMake' +easyblock = 'CMakeMake' -name = "LLVM" -version = "3.6.0" +name = 'LLVM' +version = '3.7.0' homepage = "http://llvm.org/" description = """The LLVM Core libraries provide a modern source- and target-independent @@ -19,8 +19,8 @@ source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ - ('CMake', '3.2.2'), - ('Python', '2.7.9'), + ('CMake', '3.2.3'), + ('Python', '2.7.10'), ] configopts = '-DBUILD_SHARED_LIBS=ON ' -- GitLab From 77e347d26c585e969e56c63031f9a6922fdf0b2c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 09:59:56 +0200 Subject: [PATCH 1075/1172] dcw bumped to 1.1.2 and libxml2 python pound deleted --- easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb index fbe76fab64..2d5340eaba 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.0.0-intel-2015a.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('netCDF', '4.3.3.1'), ('expat', '2.1.0'), - ('libxml2', '2.9.2', '-Python-2.7.9'), + ('libxml2', '2.9.2'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb index d06010de6a..34dae17af8 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ description = """GMT is an open source collection of about 80 command-line tools toolchain = {'name': 'intel', 'version': '2015a'} gshhg_ver = '2.3.4' -dcw_ver = '1.1.1' +dcw_ver = '1.1.2' sources = [ 'gmt-%(version)s-src.tar.bz2', # coastlines, rivers, and political boundaries -- GitLab From 39bae7324d3c6f7f6bb0221e6481fa003728ed10 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 10:11:55 +0200 Subject: [PATCH 1076/1172] added python-2.7.10 and opnssl commented out dep --- .../SCons-2.3.6-foss-2015a-Python-2.7.10.eb | 26 +++++++++++++++++++ .../SCons-2.3.6-intel-2015a-Python-2.7.10.eb | 26 +++++++++++++++++++ .../Subversion-1.8.14-foss-2015a.eb | 2 ++ 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..6056720861 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..ffd4f194b1 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb index 9bae8b637e..3d1d0481ab 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -21,6 +21,8 @@ dependencies = [ ('SQLite', '3.8.8.1'), ('zlib', '1.2.8'), ('Serf', '1.3.8'), +# ('OpenSSL', '1.0.1p'), # 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 ] configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -- GitLab From 791092bf87c2cbf6f47baef4e884bd50911cfde5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:13:26 +0200 Subject: [PATCH 1077/1172] {lang}[goolf/1.4.10] Python 2.7.10 --- .../libreadline-6.3-goolf-1.4.10.eb | 27 ++++ .../p/Python/Python-2.7.10-goolf-1.4.10.eb | 122 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 40 ++++++ .../t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb | 25 ++++ .../t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb | 24 ++++ 5 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb 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 new file mode 100644 index 0000000000..918bfc4406 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +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': '1.4.10'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb new file mode 100644 index 0000000000..5049d210bb --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +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': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +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', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % 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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + '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', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + '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', '0.7.14', { + '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', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..0687048004 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# 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', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..fe02a2bc48 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.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': 'goolf', 'version': '1.4.10'} + +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-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb new file mode 100644 index 0000000000..2b006409f0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From da2dbf7410dd71a1d0b371737acf2e329f755a5e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 10:14:23 +0200 Subject: [PATCH 1078/1172] subversion openssl put into Serf (as it should be) --- easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 2 ++ .../easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index 766c8a1db4..5df9ed21cf 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -20,6 +20,8 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), +# ('OpenSSL', '1.0.1p'), # 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')] diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb index 3d1d0481ab..9bae8b637e 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -21,8 +21,6 @@ dependencies = [ ('SQLite', '3.8.8.1'), ('zlib', '1.2.8'), ('Serf', '1.3.8'), -# ('OpenSSL', '1.0.1p'), # 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 ] configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " -- GitLab From df141640d38cdf92921bf2eff0e7079f1c23ed17 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 10:16:15 +0200 Subject: [PATCH 1079/1172] added easyblock SCons to Serf --- easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index 5df9ed21cf..febe7d2fb6 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -1,3 +1,4 @@ +easyblock = 'SCons' name = 'Serf' version = '1.3.8' -- GitLab From 9a727cc49ddf8005e3960f214eb9aff6d83aa97f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:28:00 +0200 Subject: [PATCH 1080/1172] fix/extend sanity check --- easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb index 7d14c8a252..010a358d92 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/ncap'], + 'files': ['bin/%s' % x for x in ['ncap2', 'ncatted', 'ncbo', 'ncdiff', 'ncea', 'ncecat', 'nces', 'ncflint', + 'ncks', 'ncpdq', 'ncra', 'ncrcat', 'ncrename']], 'dirs': [], } -- GitLab From 77708390964527327e99b5f80de32a740ac2ee88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:35:14 +0200 Subject: [PATCH 1081/1172] fix remark --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 1792b55d05..5cf3b03e64 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -8,8 +8,8 @@ description = """ANother Tool for Language Recognition""" toolchain = {'name': 'intel', 'version': '2014b'} -sources = ['antlr-%(version)s.tar.gz'] source_urls = ['http://www.antlr2.org/download'] +sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -- GitLab From f021c14de9bdce3ca7e7c7f0dee4c3b799bed093 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:35:28 +0200 Subject: [PATCH 1082/1172] fix remark wrt sources --- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index 3f6e01e0b7..b32cf6ce86 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -8,8 +8,8 @@ description = """ANother Tool for Language Recognition""" toolchain = {'name': 'ictce', 'version': '5.4.0'} -sources = ['antlr-%(version)s.tar.gz'] source_urls = ['http://www.antlr2.org/download'] +sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -- GitLab From 343f4e66fbf25ce25767f6c100c8d428cc383d3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:43:55 +0200 Subject: [PATCH 1083/1172] fix GMP dep in Python 2.7.10 goolf/1.4.10 easyconfig --- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb | 25 +++++++++++++++++++ .../p/Python/Python-2.7.10-goolf-1.4.10.eb | 2 +- 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.eb new file mode 100644 index 0000000000..fde2319360 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.7.2.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': 'GCC', 'version': '4.7.2'} + +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 5049d210bb..66bb207792 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), - ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto + ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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 0861cd757938bbb9f76b43cf855a4b526c9ff87a Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 11:54:18 +0300 Subject: [PATCH 1084/1172] Updating Python and Java version --- ...on-2.7.3.eb => cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb} | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb | 4 ++-- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb => cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb} (97%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb similarity index 97% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb index 8e35469e5b..1d7c0f2ab8 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://cutadapt.googlecode.com/files/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -pyver = '2.7.3' +pyver = '2.7.10' pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = "-%s-%s" % (python, pyver) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb index bd99041b10..b817c08a29 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb @@ -23,9 +23,9 @@ sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] java = 'Java' -javaver = '1.7.0_21' +javaver = '1.7.0_80' -dependencies = [('Java', '1.7.0_21', '', True)] +dependencies = [('Java', '1.7.0_80', '', True)] install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc" diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 425d2e339b..454881111b 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -17,7 +17,7 @@ install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir dependencies = [ ('FastQC', '0.10.1'), - ('cutadapt', '1.5', '-Python-2.7.3'), + ('cutadapt', '1.5', '-Python-2.7.10'), ] sanity_check_paths = { -- GitLab From 70f81f3cbcb49ea56d392b7b81b9a1055b5912f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 10:59:39 +0200 Subject: [PATCH 1085/1172] move MRO::Compat up above SQL::Abstract --- easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb index 0a30a9f307..be5cb1a1a7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb @@ -343,6 +343,10 @@ exts_list = [ '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'], + }), ('SQL::Abstract', '1.81', { 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], @@ -732,10 +736,6 @@ exts_list = [ 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], }), - ('MRO::Compat', '0.12', { - 'source_tmpl': 'MRO-Compat-0.12.tar.gz', - 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], - }), ('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'], -- GitLab From a11ae0accff4c2ca26e2e811418e494321e9b767 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 11:18:44 +0200 Subject: [PATCH 1086/1172] GCC toolchain defined for GMP --- .../CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb | 28 +++++++++++++++++++ .../CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb | 2 +- .../CGAL-4.6-intel-2015a-Python-2.7.10.eb | 28 +++++++++++++++++++ .../CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 2 +- .../MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb | 2 +- .../MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb | 2 +- 6 files changed, 60 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..2855294948 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,28 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.10' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddeps = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb index 4545d7456c..9ce79e1054 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb @@ -15,7 +15,7 @@ pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('GMP', '6.0.0a'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), ('Qt', '4.8.6', '-GLib-2.44.0'), diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f1d124d613 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,28 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.10' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddeps = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index f2b18cd866..8275e85580 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -15,7 +15,7 @@ pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('GMP', '6.0.0a'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), ('Qt', '4.8.6', '-GLib-2.44.0'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb index 3ff2a17d36..2a2f6420b3 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb @@ -18,7 +18,7 @@ gmp='GMP' gmpver='6.0.0a' versionsuffix='-%s-%s' % (gmp,gmpver) -dependencies = [(gmp, gmpver)] +dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb index 147f24acc7..c6a9305730 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb @@ -18,7 +18,7 @@ gmp='GMP' gmpver='6.0.0a' versionsuffix='-%s-%s' % (gmp,gmpver) -dependencies = [(gmp, gmpver)] +dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' -- GitLab From d9318548076e500af917be957b81e3c7048d0d03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 11:35:48 +0200 Subject: [PATCH 1087/1172] move up 'Moo', add Hash::Merge, for SQL::Abstract --- .../easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb index be5cb1a1a7..ab7a8379bf 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb @@ -347,6 +347,14 @@ exts_list = [ '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'], @@ -600,10 +608,6 @@ exts_list = [ 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], }), - ('Moo', '2.000002', { - 'source_tmpl': 'Moo-2.000002.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - }), ('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'], -- GitLab From f10238fd4dbc90de151980cf4ac39834ecc333bf Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 12:38:41 +0300 Subject: [PATCH 1088/1172] Fixing minor remarks --- .../easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb index b817c08a29..41209b695a 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb @@ -13,9 +13,9 @@ version = '0.10.1' 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.""" + 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': 'goolf', 'version': '1.4.10'} -- GitLab From 2322383dc4f743a346aa1e1ebf285b03f370ceda Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 23 Sep 2015 12:39:52 +0300 Subject: [PATCH 1089/1172] Fixing minor remarks --- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 454881111b..5620bbf4b8 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -4,9 +4,9 @@ name = 'Trim_Galore' version = '0.3.7' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' -description = """A wrapper tool around Cutadapt and FastQC to consistently apply -quality and adapter trimming to FastQ files, with some extra functionality for -MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 401516540e40d10ac587c947a74f89ecc2f7d8d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 11:57:49 +0200 Subject: [PATCH 1090/1172] use Python 2.7.10 + add missing easyconfigs for deps + fix Mesa easyconfig filename --- .../g/glproto/glproto-1.4.17-intel-2015a.eb | 21 +++++++++++++++ ...damage-1.1.4-intel-2015a-Python-2.7.10.eb} | 2 +- ...bXfont-1.5.1-intel-2015a-Python-2.7.10.eb} | 2 +- .../l/libdrm/libdrm-2.4.59-intel-2015a.eb | 27 +++++++++++++++++++ .../libpciaccess-0.13.1-intel-2015a.eb | 26 ++++++++++++++++++ ... Mesa-10.5.5-intel-2015a-Python-2.7.10.eb} | 11 +++----- .../pkg-config/pkg-config-0.28-intel-2015a.eb | 27 +++++++++++++++++++ .../xorg-macros-1.17-intel-2015a.eb | 22 +++++++++++++++ 8 files changed, 129 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb rename easybuild/easyconfigs/l/libXdamage/{libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb => libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb} (94%) rename easybuild/easyconfigs/l/libXfont/{libXfont-1.5.1-intel-2015a-Python-2.7.9.eb => libXfont-1.5.1-intel-2015a-Python-2.7.10.eb} (94%) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb rename easybuild/easyconfigs/m/Mesa/{Mesa-10.5.5-intel-2015b-Python-2.7.9.eb => Mesa-10.5.5-intel-2015a-Python-2.7.10.eb} (93%) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb 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 new file mode 100644 index 0000000000..e647894422 --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'glproto' +version = '1.4.17' + +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 = ['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-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb similarity index 94% rename from easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb index 9934005796..0cb53836e3 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libXdamage' version = '1.1.4' -versionsuffix = '-Python-2.7.9' +versionsuffix = '-Python-2.7.10' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X Damage extension library""" diff --git a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb similarity index 94% rename from easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb index 7ed47b7b55..c14d0fe75e 100644 --- a/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libXfont' version = '1.5.1' -versionsuffix = '-Python-2.7.9' +versionsuffix = '-Python-2.7.10' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X font libary""" diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb new file mode 100644 index 0000000000..584e242cbf --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.59' + +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': '2015a'} + +dependencies = [ + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] + +configopts = '--enable-nouveau-experimental-api' + +sanity_check_paths = { + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000..ce77f3502c --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +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': 'intel', 'version': '2015a'} + +builddependencies = [ + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('xorg-macros', '1.17'), +] + +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-10.5.5-intel-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb similarity index 93% rename from easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb rename to easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 33fc721a75..b00f99be5e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -7,7 +7,6 @@ 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': '2015a'} toolchainopts = {'optarch': True} @@ -17,17 +16,15 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] -pythonver = '2.7.9' +pythonver = '2.7.10' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.2'), - ('Autoconf', '2.69'), - ('Automake', '1.15'), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), ('pkg-config', '0.28'), - ('libtool', '2.4.5'), ('glproto', '1.4.17'), ('kbproto', '1.0.6'), ('xextproto', '7.3.0'), @@ -38,14 +35,14 @@ builddependencies = [ dependencies = [ ('Python', pythonver), - ('libxml2', '2.9.2', versionsuffix), + ('libxml2', '2.9.2'), ('libdrm', '2.4.59'), ('libX11', '1.6.3', versionsuffix), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4', versionsuffix), ('libXfont', '1.5.1', versionsuffix), - ('LLVM', '3.6.0'), + ('LLVM', '3.7.0'), ('eudev', '3.0'), ] diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb new file mode 100644 index 0000000000..f5981f1368 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.28' + +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).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb new file mode 100644 index 0000000000..195ab46393 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.17' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5a906cabf2b9c79138e5f64362ea1cb833f99817 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 12:22:24 +0200 Subject: [PATCH 1091/1172] Added CMake for foss-2015b --- .../c/CMake/CMake-3.3.2-foss-2015b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb new file mode 100644 index 0000000000..9d27256dc6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': '2015b'} + +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' -- GitLab From b3324aded6479df748f7015400f58fee381ce013 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 12:22:56 +0200 Subject: [PATCH 1092/1172] Added up to date MariaDB for foss/2015b --- .../m/MariaDB/MariaDB-10.0.21-foss-2015b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb new file mode 100644 index 0000000000..9d30a41238 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.0.21' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'foss' , 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('ncurses' , '5.9'), +] + +builddependencies = [ + ('CMake', '3.3.2'), +] + +configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From 63cd42db4deb76fbcf2178bd790015ccd08689fa Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 12:23:21 +0200 Subject: [PATCH 1093/1172] Removed old MariaDB easyconfigs (untested) --- .../MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb | 27 ---------------- .../m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb | 27 ---------------- .../m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb | 32 ------------------- 3 files changed, 86 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index 4615fe660c..0000000000 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MariaDB' -version = '5.5.29' - -homepage = 'https://mariadb.org/' -description = """MariaDB An enhanced, drop-in replacement for MySQL.""" - -toolchain = {'name': 'goalf' , 'version': '1.1.0-no-OFED'} - -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('ncurses' , '5.9'), -] - -builddependencies = [ - ('CMake', '2.8.4'), -] - -configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -makeopts = "VERBOSE=1" - -sanity_check_paths = { - 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], - 'dirs': ['include', 'share'], -} diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb deleted file mode 100644 index 89c5e0ba20..0000000000 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-goolf-1.4.10.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MariaDB' -version = '5.5.29' - -homepage = 'https://mariadb.org/' -description = """MariaDB An enhanced, drop-in replacement for MySQL.""" - -toolchain = {'name': 'goolf' , 'version': '1.4.10'} - -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('ncurses' , '5.9'), -] - -builddependencies = [ - ('CMake', '2.8.4'), -] - -configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -makeopts = "VERBOSE=1" - -sanity_check_paths = { - 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], - 'dirs': ['include', 'share'], -} diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb deleted file mode 100644 index 8e7fb013a4..0000000000 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MariaDB' -version = '5.5.29' - -homepage = 'https://mariadb.org/' -description = """MariaDB An enhanced, drop-in replacement for MySQL.""" - -toolchain = {'name': 'ictce' , 'version': '4.1.13'} - -sources = [SOURCELOWER_TAR_GZ] - -# this is fixed in intel 2013 series -patches = ['define_unreachable_builtin.patch'] - -dependencies = [ - ('ncurses' , '5.9'), - ('libreadline', '6.2'), -] - -builddependencies = [('CMake', '2.8.4')] - -configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -buildopts = "VERBOSE=1" - -sanity_check_paths = { - 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], - 'dirs': ['include', 'share'], -} - -moduleclass = 'data' -======= -- GitLab From 7da2065e248d276b2fb9c9f0fda5d96fa3fe04f7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 13:16:57 +0200 Subject: [PATCH 1094/1172] Added Bison for foss/2015b --- .../b/Bison/Bison-3.0.2-foss-2015b.eb | 22 ++++++++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb new file mode 100644 index 0000000000..7144e90187 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'foss', 'version': '2015b'} + +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/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb new file mode 100644 index 0000000000..b66775c7a6 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.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': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 997f04c07278bd1cd75d8e5d607eb565d7f2565f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 13:19:52 +0200 Subject: [PATCH 1095/1172] Added source_url to MariaDB --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb index 9d30a41238..fafb43db20 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb @@ -9,6 +9,7 @@ description = """MariaDB An enhanced, drop-in replacement for MySQL.""" toolchain = {'name': 'foss' , 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] +source_url = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ ('ncurses' , '5.9'), @@ -16,6 +17,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.3.2'), + ('Bison', '3.0.2'), ] configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -- GitLab From 61e2271c0792d0cbf1c6f70c050c554afcaf16ef Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 13:20:06 +0200 Subject: [PATCH 1096/1172] Restore MariaDB-5.5.29-ictce-4.1.13.eb --- .../m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb new file mode 100644 index 0000000000..63213cd9a5 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '5.5.29' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'ictce' , 'version': '4.1.13'} + +sources = [SOURCELOWER_TAR_GZ] + +# this is fixed in intel 2013 series +patches = ['define_unreachable_builtin.patch'] + +dependencies = [ + ('ncurses' , '5.9'), + ('libreadline', '6.2'), +] + +builddependencies = [('CMake', '2.8.4')] + +configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +buildopts = "VERBOSE=1" + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From e6fbbe08b6f3ff65c9dd3ab3094dad1ff43dc0a1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 14:16:57 +0200 Subject: [PATCH 1097/1172] Added libedit BSD replacement for libreadline --- .../libedit-20150325-GNU-4.9.3-2.25.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..fe54474a05 --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20150325' + +homepage = 'http://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = ['libedit-20150325-3.1.tar.gz'] +source_urls = ['http://thrysoee.dk/editline/'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.so', 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From c9eac96c1d9aaad05930c2d23a009544b2724ebb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 14:18:33 +0200 Subject: [PATCH 1098/1172] Mariadb: use libedit --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb index fafb43db20..b48e116f8f 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb @@ -12,7 +12,8 @@ sources = [SOURCELOWER_TAR_GZ] source_url = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ - ('ncurses' , '5.9'), + ('ncurses' , '5.9', '', ('GNU', '4.9.3-2.25')), + ('libedit', '20150325', '', ('GNU', '4.9.3-2.25')), ] builddependencies = [ -- GitLab From 012627b732a6a482c2847d5d90ee85b3cf384795 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 14:28:59 +0200 Subject: [PATCH 1099/1172] Removed needless space --- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index 5620bbf4b8..53e79949f3 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'Trim_Galore' version = '0.3.7' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' - description = """A wrapper tool around Cutadapt and FastQC to consistently apply +description = """A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" -- GitLab From 827dce2eeaa13450a3967d003ba2a266e9230b05 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 14:32:42 +0200 Subject: [PATCH 1100/1172] added newer versions of RAxML easyconfigs. switches to MakeCp easyblock --- .../RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb | 29 +++++++++++++++++++ .../RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb | 29 +++++++++++++++++++ .../RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb | 29 +++++++++++++++++++ .../RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb | 29 +++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb new file mode 100644 index 0000000000..34e93e35d8 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb @@ -0,0 +1,29 @@ +# 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 = 'RAxML' +version = '8.1.1' +versionsuffix ='-mpi-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = ' -f Makefile.AVX.MPI.gcc' + +files_to_copy = [(["raxmlHPC-MPI-AVX"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-MPI-AVX"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb new file mode 100644 index 0000000000..42ce2e4fdd --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb @@ -0,0 +1,29 @@ +# 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 = 'RAxML' +version = '8.1.1' +versionsuffix ='-mpi-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = ' -f Makefile.SSE3.MPI.gcc' + +files_to_copy = [(["raxmlHPC-MPI-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-MPI-SSE3"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb new file mode 100644 index 0000000000..09ffafe613 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb @@ -0,0 +1,29 @@ +# 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 = 'RAxML' +version = '8.1.1' +versionsuffix ='-mt-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = '-f Makefile.AVX.PTHREADS.gcc' + +files_to_copy = [(["raxmlHPC-PTHREADS-AVX"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-PTHREADS-AVX"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb new file mode 100644 index 0000000000..305c9c94a6 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb @@ -0,0 +1,29 @@ +# 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 = 'RAxML' +version = '8.1.1' +versionsuffix ='-mt-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = '-f Makefile.SSE3.PTHREADS.gcc' + +files_to_copy = [(["raxmlHPC-PTHREADS-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 2125bef2438e6c18d28b724c0f1ca90746ddb7b3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 14:37:34 +0200 Subject: [PATCH 1101/1172] Fix typos in MariaDB --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb index b48e116f8f..f1aa111e06 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb @@ -9,7 +9,7 @@ description = """MariaDB An enhanced, drop-in replacement for MySQL.""" toolchain = {'name': 'foss' , 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] -source_url = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] +source_urls = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ ('ncurses' , '5.9', '', ('GNU', '4.9.3-2.25')), @@ -18,7 +18,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.3.2'), - ('Bison', '3.0.2'), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), ] configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -- GitLab From da03171998642c4230f476931c724f0880b74645 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 14:50:11 +0200 Subject: [PATCH 1102/1172] added weka easyconfig --- .../w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb new file mode 100644 index 0000000000..d85051f5d4 --- /dev/null +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'WEKA' +version = '3.6.12' +versionsuffix = '-Java-1.7.0_80' + +homepage = 'http://www.cs.waikato.ac.nz/ml/weka/index.html' +description = """ Weka is a collection of machine learning algorithms for data mining tasks. + The algorithms can either be applied directly to a dataset or called from your own Java code. + Weka contains tools for data pre-processing, classification, regression, clustering, + association rules, and visualization. It is also well-suited for developing new machine + learning schemes.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://prdownloads.sourceforge.net/weka/'] +sources = ['%s-%s.zip' % (name.lower(), version.replace('.','-'))] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ["weka.jar"], + 'dirs': [""] +} + +modextravars = { + 'WEKAINSTALL': '$root', +} + +modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " + +moduleclass = 'bio' -- GitLab From 371a998539b3d8d5f80ef674210d32b3b966239b Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 14:52:48 +0200 Subject: [PATCH 1103/1172] added Trimmomatic easyconfig --- .../Trimmomatic-0.32-Java-1.7.0_80.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb new file mode 100644 index 0000000000..a89bd3216a --- /dev/null +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.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 = 'Tarball' + +name = 'Trimmomatic' +version = '0.32' + +homepage = 'http://www.usadellab.org/cms/?page=trimmomatic' +description = """Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and their associated + parameters are supplied on the command line. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] +sources = [SOURCE_ZIP] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute Trimmomatic run: java -jar \\$EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From 9e9e3046df5f49f3045f700dc12716bd6bca647c Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 14:56:46 +0200 Subject: [PATCH 1104/1172] renamed file --- .../PBZIP2/{1.1.8-ictce-6.2.5.eb => PBZIP2-1.1.8-ictce-6.2.5.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PBZIP2/{1.1.8-ictce-6.2.5.eb => PBZIP2-1.1.8-ictce-6.2.5.eb} (100%) diff --git a/easybuild/easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb similarity index 100% rename from easybuild/easyconfigs/p/PBZIP2/1.1.8-ictce-6.2.5.eb rename to easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb -- GitLab From c10ab4dca71441e8f43a8e7c7b2c5ddb9dd9b3e3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 14:57:09 +0200 Subject: [PATCH 1105/1172] removed line at end --- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb index e0710326fb..1344df3f17 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -27,8 +27,7 @@ files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "Cha sanity_check_paths = { 'files': ["bin/pbzip2"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'tools' - -- GitLab From 0c1e7d99278d30d2c46821952dbaae406c86d61b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 15:00:39 +0200 Subject: [PATCH 1106/1172] Move MariaDB to GNU toolchain --- .../c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb | 31 +++++++++++++++++++ ...b.eb => MariaDB-10.0.21-GNU-4.9.3-2.25.eb} | 8 ++--- 2 files changed, 35 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb rename easybuild/easyconfigs/m/MariaDB/{MariaDB-10.0.21-foss-2015b.eb => MariaDB-10.0.21-GNU-4.9.3-2.25.eb} (75%) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..b78673a828 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': 'GNU', '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', '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/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb similarity index 75% rename from easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb rename to easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb index f1aa111e06..fb035bc64f 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-foss-2015b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -6,19 +6,19 @@ version = '10.0.21' homepage = 'https://mariadb.org/' description = """MariaDB An enhanced, drop-in replacement for MySQL.""" -toolchain = {'name': 'foss' , 'version': '2015b'} +toolchain = {'name': 'GNU' , 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ - ('ncurses' , '5.9', '', ('GNU', '4.9.3-2.25')), - ('libedit', '20150325', '', ('GNU', '4.9.3-2.25')), + ('ncurses' , '5.9'), + ('libedit', '20150325'), ] builddependencies = [ ('CMake', '3.3.2'), - ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4'), ] configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" -- GitLab From 8fb98538968501e2135465a3c6433e0491191a0e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2015 16:32:07 +0200 Subject: [PATCH 1107/1172] noveau deleted --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb index 584e242cbf..3b516fcaac 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb @@ -16,12 +16,10 @@ dependencies = [ ('libpciaccess', '0.13.1'), ] -configopts = '--enable-nouveau-experimental-api' - sanity_check_paths = { 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } moduleclass = 'lib' -- GitLab From 090abe22c00ad62318ae377f1bf6cc07b272d787 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 16:45:26 +0200 Subject: [PATCH 1108/1172] Extend dependencies of MariaDB --- .../l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb | 28 +++++++++++++++++++ .../MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb | 5 ++++ .../z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb | 21 ++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..aa7e3a4527 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +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': 'GNU', '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' + +dependencies = [('zlib', '1.2.8')] + +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/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb index fb035bc64f..b51de010cd 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -12,8 +12,10 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] dependencies = [ + ('zlib', '1.2.8'), ('ncurses' , '5.9'), ('libedit', '20150325'), + ('libxml2', '2.9.2'), ] builddependencies = [ @@ -21,6 +23,9 @@ builddependencies = [ ('Bison', '3.0.4'), ] +# remove prebundled version of libedit +preconfigopts = "rm -rf cmd-line-utils && " + configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..5390ac9f19 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +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': 'GNU', 'version': '4.9.3-2.25'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 29a60df5fa79d4902c32b49b6bb43b9ad2791cdd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Sep 2015 17:10:24 +0200 Subject: [PATCH 1109/1172] Do not use ld.gold for MariaDB --- .../easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb index b51de010cd..3284f299e7 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -27,6 +27,8 @@ builddependencies = [ preconfigopts = "rm -rf cmd-line-utils && " configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +# do not use ld.gold +configopts += " -DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], -- GitLab From bdbfce6826e87bb545f5970b3f82ebf54f7f0b86 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 17:43:54 +0200 Subject: [PATCH 1110/1172] removed last line --- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb index b66756cb0a..697d896974 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb @@ -31,4 +31,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From e446404e0663dc3a96c6734aba59fd95db67ee40 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 17:44:18 +0200 Subject: [PATCH 1111/1172] switch to buildopts --- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb index 697d896974..52832136b4 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://compression.ca/pbzip2/'] sources = [SOURCELOWER_TAR_GZ] -makeopts = ' CC=$CXX' +buildopts = ' CC=$CXX' parallel = 1 diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb index 1344df3f17..ce2a575604 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['http://compression.ca/pbzip2/'] sources = [SOURCELOWER_TAR_GZ] -makeopts = ' CC=$CXX' +buildopts = ' CC=$CXX' parallel = 1 -- GitLab From 4b9c2cad6531fe4c0abcb28cc78ad5cbc6a79409 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 23 Sep 2015 18:20:36 +0200 Subject: [PATCH 1112/1172] removed empty lines --- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb | 3 +-- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index bda774ae23..54d6c62fe8 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -17,7 +17,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] @@ -33,4 +33,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index 2a4076857e..131cf3480b 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -17,7 +17,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] @@ -33,4 +33,3 @@ modextrapaths = { } moduleclass = 'bio' - -- GitLab From b0cc9758ee6a518e68af9b90aa95c0d8bbe25f72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 20:34:37 +0200 Subject: [PATCH 1113/1172] fix style issues --- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb | 2 +- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index 54d6c62fe8..97ac63797e 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] sanity_check_paths = { 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], - 'dirs': [""] + 'dirs': [], } # add the installation dir to PATH diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index 131cf3480b..5be4f1c43e 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] sanity_check_paths = { 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], - 'dirs': [""] + 'dirs': [], } # add the installation dir to PATH -- GitLab From 36978f3ceca40b4343a8dca1c51e0d24048ca420 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 20:42:58 +0200 Subject: [PATCH 1114/1172] minor style fixs --- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb index 52832136b4..e0822f5ef3 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://compression.ca/pbzip2/'] sources = [SOURCELOWER_TAR_GZ] -buildopts = ' CC=$CXX' +buildopts = " CC=$CXX" parallel = 1 @@ -27,7 +27,7 @@ files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "Cha sanity_check_paths = { 'files': ["bin/pbzip2"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb index ce2a575604..a1befffbe4 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['http://compression.ca/pbzip2/'] sources = [SOURCELOWER_TAR_GZ] -buildopts = ' CC=$CXX' +buildopts = " CC=$CXX" parallel = 1 -- GitLab From 97f9a22b9f5889e376675f6812a6946bcfc7b6a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2015 20:45:51 +0200 Subject: [PATCH 1115/1172] fix versionsuffix --- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb | 4 ++-- easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index 97ac63797e..c965b7304f 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -7,7 +7,7 @@ easyblock = "Tarball" name = 'SSAHA2' version = '2.5.5' -versionsuffix = "_i686" +versionsuffix = '-i686' homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a @@ -20,7 +20,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is toolchain = {'name': 'dummy', 'version': ''} source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] -sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] +sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] sanity_check_paths = { 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index 5be4f1c43e..bb97c237d9 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -7,7 +7,7 @@ easyblock = "Tarball" name = 'SSAHA2' version = '2.5.5' -versionsuffix = "_x86_64" +versionsuffix = '-x86_64' homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a @@ -20,7 +20,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is toolchain = {'name': 'dummy', 'version': ''} source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] -sources = ['%(namelower)s_v%(version)s%(versionsuffix)s.tgz'] +sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] sanity_check_paths = { 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], -- GitLab From d279fcbc68a309492c1bf6f49c4d6ac7f2a37dab Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2015 11:54:21 +0200 Subject: [PATCH 1116/1172] Comments implemented --- .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb | 1 + .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 1 + easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb | 2 +- easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb | 2 +- .../easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb | 1 + .../easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb | 1 + 6 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb index f1d124d613..118c4c33e9 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb @@ -15,6 +15,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ +#GMP does not compile correctly with ICC on Haswell architecture ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index 8275e85580..63a7708ff6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -15,6 +15,7 @@ pythonversion = '2.7.9' versionsuffix = "-Python-%s" % pythonversion dependencies = [ +#GMP does not compile correctly with ICC on Haswell architecture ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.58.0', versionsuffix), ('MPFR', '3.1.2', '-GMP-6.0.0a'), diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb index 209f2f13dd..e2971ec78c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-foss-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -sources = ['glib-%(version)s.tar.xz'] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb index 345c9887e6..224be43936 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] -sources = ['glib-%(version)s.tar.xz'] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb index 2a2f6420b3..c0d8ea5a48 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb @@ -18,6 +18,7 @@ gmp='GMP' gmpver='6.0.0a' versionsuffix='-%s-%s' % (gmp,gmpver) +#GMP does not compile correctly with ICC on Haswell architecture dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb index c6a9305730..4afd6ab5dc 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb @@ -18,6 +18,7 @@ gmp='GMP' gmpver='6.0.0a' versionsuffix='-%s-%s' % (gmp,gmpver) +#GMP does not compile correctly with ICC on Haswell architecture dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] runtest = 'check' -- GitLab From 6db8d3faff13fc22d5f0141c04a7437c3f90dad0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2015 11:59:03 +0200 Subject: [PATCH 1117/1172] roll back to LLVM 3.6.2 --- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 b00f99be5e..98e47f7b5b 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 @@ -42,7 +42,7 @@ dependencies = [ ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4', versionsuffix), ('libXfont', '1.5.1', versionsuffix), - ('LLVM', '3.7.0'), + ('LLVM', '3.6.2'), ('eudev', '3.0'), ] -- GitLab From 028f92abe40475e07d6ee001bc27f5d9b53a0632 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2015 12:02:27 +0200 Subject: [PATCH 1118/1172] LLVM362 --- .../l/LLVM/LLVM-3.6.2-intel-2015a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb new file mode 100644 index 0000000000..0e2be216c9 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.6.2' + +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': '2015a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.2.3'), + ('Python', '2.7.10'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files' : ['bin/llvm-ar'], + 'dirs' : ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 964916242b6aa36ff074fe4c8eb84b53265f8f4f Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 24 Sep 2015 18:17:55 +0200 Subject: [PATCH 1119/1172] removed the harcoded java version in versionsuffix --- easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index d85051f5d4..4d0ead5359 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -7,7 +7,6 @@ easyblock = "Tarball" name = 'WEKA' version = '3.6.12' -versionsuffix = '-Java-1.7.0_80' homepage = 'http://www.cs.waikato.ac.nz/ml/weka/index.html' description = """ Weka is a collection of machine learning algorithms for data mining tasks. @@ -21,7 +20,11 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://prdownloads.sourceforge.net/weka/'] sources = ['%s-%s.zip' % (name.lower(), version.replace('.','-'))] -dependencies = [('Java', '1.7.0_80')] +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] sanity_check_paths = { 'files': ["weka.jar"], -- GitLab From c8fad2c01d91975a03af7c711b8ff1418a16a196 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 24 Sep 2015 18:18:22 +0200 Subject: [PATCH 1120/1172] style fixes for sanity check --- easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 4d0ead5359..17e72b0628 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -28,7 +28,7 @@ dependencies = [(java, javaver)] sanity_check_paths = { 'files': ["weka.jar"], - 'dirs': [""] + 'dirs': [] } modextravars = { -- GitLab From 3ed972bbd572690024e9579ff9e2f3f0ce41ebc6 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 24 Sep 2015 18:19:07 +0200 Subject: [PATCH 1121/1172] style fix --- easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 17e72b0628..a65ca2295b 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ description = """ Weka is a collection of machine learning algorithms for data m toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://prdownloads.sourceforge.net/weka/'] -sources = ['%s-%s.zip' % (name.lower(), version.replace('.','-'))] +sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] java = 'Java' javaver = '1.7.0_80' -- GitLab From 5a3a58cedb04ab1de13c096a138326c94c30d158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2015 21:18:40 +0200 Subject: [PATCH 1122/1172] {devel}[GNU/4.9.3-2.25] CMake 3.3.2 + ncurses 6.0 --- .../c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb | 31 +++++++++++++++++ .../n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 34 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..c4400508b1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': 'GNU', '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', '1.0.1p'), +] + +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/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..6d33835f96 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-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': 'GNU', '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", "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' -- GitLab From daf360b0e7b3542010275880767fa8923cbe34ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2015 21:33:22 +0200 Subject: [PATCH 1123/1172] stick to ncurses 5.9, for now --- easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb index c4400508b1..86f4ad5681 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' dependencies = [ - ('ncurses', '6.0'), + ('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'), -- GitLab From 63352c66558a2b34583fa22697fa893995bccf81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2015 21:36:21 +0200 Subject: [PATCH 1124/1172] fix typo --- easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 6d33835f96..4012f0e69b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -23,7 +23,7 @@ configopts = [ libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + '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']] + -- GitLab From b9c0485b585380b7aec0918515fd64c21bd302fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 24 Sep 2015 21:34:48 +0200 Subject: [PATCH 1125/1172] Downgrade to ncurses 5.9 to avoid trouble We will make the switch with 2016 toolchains --- .../easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 cdddedcca0..1247037f85 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 @@ -17,7 +17,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] preconfigopts = " LDFLAGS='-ltinfo' " -dependencies = [('ncurses', '6.0')] +dependencies = [('ncurses', '5.9')] sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index 6c283693fb..6ce1637771 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -16,7 +16,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8', '', ('GCC', '4.9.3-binutils-2.25')), ('libreadline', '6.3'), - ('ncurses', '6.0'), + ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -- GitLab From 08b6fd38b56ec797c4d8f30c3d74247815726137 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2015 21:56:51 +0200 Subject: [PATCH 1126/1172] {data}[intel/2015b] DBD-mysql 4.032 --- ...DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb | 31 ++++++++++++++++ .../l/libevent/libevent-2.0.22-intel-2015b.eb | 19 ++++++++++ .../MySQL-5.6.26-intel-2015b-clientonly.eb | 36 +++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb create mode 100644 easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb new file mode 100644 index 0000000000..c3bb2969b2 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.032' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('MySQL', '5.6.26', '-clientonly'), +] + +options = {'modulename': 'DBD::mysql'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql' % (perlmajver, perlver)], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb new file mode 100644 index 0000000000..f98af9f6bf --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb @@ -0,0 +1,19 @@ +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': 'intel', 'version': '2015b'} + +source_urls = [ + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/downloads/%(name)s/%(name)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb new file mode 100644 index 0000000000..44516b2440 --- /dev/null +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'MySQL' +version = '5.6.26' +versionsuffix = '-clientonly' + +homepage = 'http://www.mysql.com/' +description = """MySQL is (as of March 2014) the world's second most widely used + open-source relational database management system (RDBMS).""" + +source_urls = ['http://dev.mysql.com/get/Downloads/MySQL-%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015b'} + +dependencies = [ + ('libevent', '2.0.22'), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), +] + +configopts = "-DWITHOUT_SERVER=ON " + +sanity_check_paths = { + 'files': ['bin/mysql'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 56ca946a44a17864d0aa4ae524f226ac7e6badb8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2015 22:02:59 +0200 Subject: [PATCH 1127/1172] fix libreadline, use GNU/4.9.3-2.25 --- .../libreadline-6.3-GCC-4.9.3-2.25.eb | 27 +++++++++++++++++++ .../MySQL-5.6.26-intel-2015b-clientonly.eb | 2 +- 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..2ce314afab --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,27 @@ +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': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb index 44516b2440..dd3b82161b 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} dependencies = [ ('libevent', '2.0.22'), - ('libreadline', '6.3'), + ('libreadline', '6.3', '', ('GNU', '4.9.3-2.25')), ('zlib', '1.2.8'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons ] -- GitLab From eac4e599914e492d2dad82feebf52652e9c6208c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 09:50:06 +0200 Subject: [PATCH 1128/1172] kick out wrong named libreadline easyconfig --- .../libreadline-6.3-GCC-4.9.3-2.25.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb deleted file mode 100644 index 2ce314afab..0000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb +++ /dev/null @@ -1,27 +0,0 @@ -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': 'GNU', 'version': '4.9.3-2.25'} -toolchainopts = {'pic': True} - -sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftp.gnu.org/gnu/readline'] - -dependencies = [('ncurses', '5.9')] - -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' -- GitLab From ceda53307187aab9706c832fecd797d8583bf297 Mon Sep 17 00:00:00 2001 From: molden Date: Fri, 25 Sep 2015 10:25:43 +0200 Subject: [PATCH 1129/1172] minor fixes --- easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb index 8c6a7116f3..aeb9e7c8b0 100644 --- a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -9,7 +9,7 @@ description = """Apache HBase. is the Hadoop database, a distributed, scalable, toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin.tar.gz'] -source_urls = ['http://www.us.apache.org/dist/hbase/hbase-1.0.2/'] +source_urls = ['http://www.us.apache.org/dist/hbase/hbase-%(version)s/'] dependencies = [('Java', '1.7.0_80')] @@ -17,7 +17,7 @@ parallel = 1 sanity_check_paths = { 'files': ["bin/hbase"], - 'dirs': ["bin","conf","docs","hbase-webapps","lib"] + 'dirs': ["conf", "docs", "hbase-webapps", "lib"] } modextravars = {'HBASE_HOME': '%(installdir)s'} -- GitLab From d97c9d6a8095a6a2df6061a23122dce0ab3e955c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 25 Sep 2015 11:33:53 +0200 Subject: [PATCH 1130/1172] Confilcts solved --- ...libXext-1.3.3-intel-2015a-Python-2.7.10.eb | 35 +++++++++++++++++++ .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 10 +++--- 2 files changed, 40 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb 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 new file mode 100644 index 0000000000..a959a12b0a --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), + ('libXdmcp', '1.1.2'), +] + +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/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 98e47f7b5b..9f2977a63e 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 @@ -21,16 +21,16 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.2'), + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ('Autotools', '20150119', '', ('GCC', '4.9.2')), - ('pkg-config', '0.28'), + ('pkg-config', '0.28', '', ('GCC', '4.9.2')), ('glproto', '1.4.17'), ('kbproto', '1.0.6'), ('xextproto', '7.3.0'), ('xproto', '7.0.27'), ('makedepend', '1.0.5'), - ('M4', '1.4.17'), + ('M4', '1.4.17', '', ('GCC', '4.9.2')), ] dependencies = [ @@ -38,7 +38,7 @@ dependencies = [ ('libxml2', '2.9.2'), ('libdrm', '2.4.59'), ('libX11', '1.6.3', versionsuffix), - ('libXext', '1.3.3'), + ('libXext', '1.3.3', versionsuffix), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4', versionsuffix), ('libXfont', '1.5.1', versionsuffix), -- GitLab From 97b2ebc1b7da579e81eb6156eed1abee6d4173e2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 25 Sep 2015 11:49:38 +0200 Subject: [PATCH 1131/1172] builddependencies it is --- .../easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb index 2855294948..624902da11 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb @@ -21,7 +21,7 @@ dependencies = [ ('Qt', '4.8.6', '-GLib-2.44.0'), ] -builddeps = [ +builddependencies = [ ('CMake', '3.1.3'), ] diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb index 9ce79e1054..9226ece655 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb @@ -21,7 +21,7 @@ dependencies = [ ('Qt', '4.8.6', '-GLib-2.44.0'), ] -builddeps = [ +builddependencies = [ ('CMake', '3.1.3'), ] diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb index 118c4c33e9..e6ea4f81d2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ ('Qt', '4.8.6', '-GLib-2.44.0'), ] -builddeps = [ +builddependencies = [ ('CMake', '3.1.3'), ] diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb index 63a7708ff6..adb6a38167 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -22,7 +22,7 @@ dependencies = [ ('Qt', '4.8.6', '-GLib-2.44.0'), ] -builddeps = [ +builddependencies = [ ('CMake', '3.1.3'), ] -- GitLab From 2552dc312951b896e2c59bd03c8199cc85e7b256 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 25 Sep 2015 12:09:02 +0200 Subject: [PATCH 1132/1172] toolchainopts puc ture added --- .../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 1 + .../easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 1 + .../l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 1 + .../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 1 + .../l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb | 1 + .../l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 1 + .../l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 1 + .../easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 1 + .../easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 1 + .../easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb | 1 + .../easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 1 + .../l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb | 1 + .../l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb | 1 + .../l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb | 1 + easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb | 1 + 40 files changed, 40 insertions(+) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 254704e224..22eb3e4fce 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 3d078ed6cf..7557598cd6 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index 33c6ee44e2..60c64c147d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,6 +5,7 @@ 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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 d35a5afd09..53eca5aa25 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 @@ -7,6 +7,7 @@ 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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index 2cbd068791..3e93f2c23c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 111dd07ee9..36c184b95a 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index 2e200ff747..5c84637a7e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index 2e16511fc4..47ab2a1eaf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 8718a3c0cd..0297dc62f1 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index dd8fbb563c..b747d1108f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 5f8aa9158f..461d52a9c8 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 df4be8cc11..9780466535 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 @@ -7,6 +7,7 @@ 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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 ddb04fedc9..f10ab602a5 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 2d7551a78a..5d91dfdb96 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 f6b392b5e3..e91eeeeabc 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 528265c88b..f98f4a1b67 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'gmpolf', 'version': '1.4.8'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 d743e7f4c4..728af8a946 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 824084e03a..ddfc201d2d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 96f39c944c..04f39a5a5e 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 35fadff4ea..85c8e40fd5 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index a36d6bdb32..dc6262f297 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 51cf5a1ff9..63cf588844 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 28520b4f81..5849c68e0b 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb index 0c0ab111ee..00ef91bfbe 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.2.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 d80e534ea6..6454b3c5bc 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 @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', 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 index 69506204a7..8b4ebb1f97 100644 --- 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 @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 69319cf49a..32892101eb 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index cd4bbd99a0..4ca7d2ddd7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index 3a42235cf9..0fdd037332 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index d446d4e3c6..4f3853dc8b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index fa340e7e85..60f233de3e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -9,6 +9,7 @@ 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/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb index 1c90dac8b1..4af0891c8a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index ae74326843..f85a2b6171 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb index 906e3a297c..8b3729f893 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index 94f3df39be..22b9077737 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 215198c95a..22727637dc 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb index da461a3caf..e102ff79f5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb index 59d56c4c28..da831a62f3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 2857dd4e54..c052dd338d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb index 70be4707e2..6b29a23daa 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', -- GitLab From 77db5dfd3b2bc66381e48e8df619b8b4c6a8624e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 25 Sep 2015 12:19:13 +0200 Subject: [PATCH 1133/1172] Nooveau deleted + some polishing --- .../libdrm-2.4.27-goalf-1.1.0-no-OFED.eb | 20 ++++++++---------- .../l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb | 19 ++++++++--------- .../l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb | 20 ++++++++---------- .../l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb | 10 ++++----- .../l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb | 21 ++++++++----------- .../l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb | 10 ++++----- 6 files changed, 44 insertions(+), 56 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb index 5c7544aa88..92ffc337dd 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb index e4bdd39b89..b1d2fbfdf4 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb @@ -6,21 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb index d970534cf1..c3030842e9 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '4.0.6'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '4.0.6'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb index 844b065646..153b29cec1 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '4.1.13'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '4.1.13'} - dependencies = [ ('libpthread-stubs', '0.3'), ('libpciaccess', '0.13.1'), ] -configopts = '--enable-nouveau-experimental-api' - sanity_check_paths = { 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb index e1a66cadcc..c5883cb6db 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb @@ -6,23 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb index 1e464e3679..d46e9edefe 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '5.5.0'} - dependencies = [ ('libpthread-stubs', '0.3'), ('libpciaccess', '0.13.1'), ] -configopts = '--enable-nouveau-experimental-api' - sanity_check_paths = { 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } moduleclass = 'lib' -- GitLab From 64b46e491bc378dde2ebdcce9e50a927a3fbbc89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 13:57:42 +0200 Subject: [PATCH 1134/1172] {bio}[intel2015b] Sailfish 0.7.4 --- .../Boost-1.59.0-intel-2015b-Python-2.7.10.eb | 25 +++++++++++++ .../g/g2log/g2log-1.0-intel-2015b.eb | 29 +++++++++++++++ .../Jellyfish/Jellyfish-2.2.0-intel-2015b.eb | 28 +++++++++++++++ ...ailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 35 +++++++++++++++++++ easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb | 24 +++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..d65dc97c6c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb new file mode 100644 index 0000000000..882630ea20 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'g2log' +version = '1.0' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), +] + +start_dir = 'g2log' +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb new file mode 100644 index 0000000000..504c9b0c81 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb @@ -0,0 +1,28 @@ +# 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 = '2.2.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000..20a55f9da7 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Sailfish' +version = '0.7.4' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), +] + +dependencies = [ + ('Boost', '1.59.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), + ('Jellyfish', '2.2.0'), + ('g2log', '1.0'), +] + +preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb new file mode 100644 index 0000000000..5f191834c6 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb @@ -0,0 +1,24 @@ +name = 'tbb' +version = '4.4.0.109' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_%(name)s_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' -- GitLab From 27065621d6827f481024dab8b1649d43317c9d42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 14:01:53 +0200 Subject: [PATCH 1135/1172] remove easyconfig for tbb 4.4.x, stick to 4.3.6.211 --- ...ailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb | 24 ------------------- 2 files changed, 1 insertion(+), 25 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 20a55f9da7..46d1bc98a1 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.0.5.339', '', True), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.0'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb deleted file mode 100644 index 5f191834c6..0000000000 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.0.109.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'tbb' -version = '4.4.0.109' - -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) - is a widely used, award-winning C++ template library for creating reliable, - portable, and scalable parallel applications. - Use Intel TBB for a simple and rapid way of developing robust task-based - parallel applications that scale to available processor cores, are compatible - with multiple environments, and are easier to maintain. - Intel TBB is the most proficient way to implement future-proof parallel applications - that tap into the power and performance of multicore and manycore hardware platforms.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['l_%(name)s_%(version)s.tgz'] - -dontcreateinstalldir = 'True' - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'lib' -- GitLab From 9b3be8b48c5e2a1dca188cf63be77602705711fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 14:26:17 +0200 Subject: [PATCH 1136/1172] don't use CMake with subtoolchain, clashes with ncurses loaded by Python (sub)dep --- .../c/CMake/CMake-3.3.2-intel-2015b.eb | 31 +++++++++++++++++++ ...ailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb new file mode 100644 index 0000000000..ba3ca2e1aa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': '2015b'} + +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/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 46d1bc98a1..a3a9a7e926 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -17,7 +17,7 @@ pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) builddependencies = [ - ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), + ('CMake', '3.3.2'), ] dependencies = [ -- GitLab From bfc2dfa0e8352611d80f6060b94c2a3d9f4f29e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 14:32:37 +0200 Subject: [PATCH 1137/1172] fix (very) minor style issues in Qt easyconfigs --- .../easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb | 6 +++--- .../easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb index 9fce73a06d..3832143476 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb @@ -12,9 +12,9 @@ source_urls = [ ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -glib='GLib' -glibver='2.44.0' -versionsuffix="-%s-%s" % (glib,glibver) +glib = 'GLib' +glibver = '2.44.0' +versionsuffix = "-%s-%s" % (glib, glibver) dependencies = [(glib, glibver)] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb index 0b1ba51db0..3c920b2a40 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb @@ -14,9 +14,9 @@ sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] patches = ['Qt-4.8.6_icc-qUnused.patch'] -glib='GLib' -glibver='2.44.0' -versionsuffix="-%s-%s" % (glib,glibver) +glib = 'GLib' +glibver = '2.44.0' +versionsuffix = "-%s-%s" % (glib, glibver) dependencies = [(glib, glibver)] -- GitLab From 84538d37608ceeaf27fae4e11b572451a8158cf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 14:58:54 +0200 Subject: [PATCH 1138/1172] use GNU toolchain for MySQL easyconfig --- ...DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb | 2 +- .../l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 2 +- ...b.eb => libevent-2.0.22-GNU-4.9.3-2.25.eb} | 4 ++-- ...MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb} | 6 +++--- .../z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb | 21 +++++++++++++++++++ 5 files changed, 28 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/l/libevent/{libevent-2.0.22-intel-2015b.eb => libevent-2.0.22-GNU-4.9.3-2.25.eb} (91%) rename easybuild/easyconfigs/m/MySQL/{MySQL-5.6.26-intel-2015b-clientonly.eb => MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb} (83%) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb index c3bb2969b2..0496e7650c 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb @@ -17,7 +17,7 @@ versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ (perl, perlver), - ('MySQL', '5.6.26', '-clientonly'), + ('MySQL', '5.6.26', '-clientonly', ('GNU', '4.9.3-2.25')), ] options = {'modulename': 'DBD::mysql'} diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index 75b8531ffa..b12575ef89 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -11,8 +11,8 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = [ - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', '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'] diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb similarity index 91% rename from easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb rename to easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb index f98af9f6bf..3b555aa6f7 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb @@ -8,11 +8,11 @@ description = """The libevent API provides a mechanism to execute a callback fun 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': 'intel', 'version': '2015b'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = [ - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', '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'] diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb similarity index 83% rename from easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb rename to easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb index dd3b82161b..d630176fd8 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-intel-2015b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -11,11 +11,11 @@ description = """MySQL is (as of March 2014) the world's second most widely used source_urls = ['http://dev.mysql.com/get/Downloads/MySQL-%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'intel', 'version': '2015b'} +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [ ('libevent', '2.0.22'), - ('libreadline', '6.3', '', ('GNU', '4.9.3-2.25')), + ('libreadline', '6.3'), ('zlib', '1.2.8'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons ] @@ -23,7 +23,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] builddependencies = [ - ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), + ('CMake', '3.3.2'), ] configopts = "-DWITHOUT_SERVER=ON " diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000..5390ac9f19 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +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': 'GNU', 'version': '4.9.3-2.25'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 1db0114e05c87dbe3e3b78d67be687c6044df739 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 15:29:21 +0200 Subject: [PATCH 1139/1172] add patch to bypass failing C++11 check in Sailfish --- .../Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 ++ .../Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch | 12 ++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index a3a9a7e926..198925231e 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['Sailfish-%(version)s_bypass-C++11-check.patch'] + python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch new file mode 100644 index 0000000000..b44441022a --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch @@ -0,0 +1,12 @@ +--- CMakeLists.txt.orig 2015-09-25 14:52:46.821073663 +0200 ++++ CMakeLists.txt 2015-09-25 14:55:23.814696637 +0200 +@@ -119,7 +119,8 @@ + set (PTHREAD_LIB "pthread") + endif() + else () +- message(FATAL_ERROR "Your C++ compiler does not support C++11.") ++ #message(FATAL_ERROR "Your C++ compiler does not support C++11.") ++ message(WARNING "Uknown C++ compiler (${CMAKE_CXX_COMPILER_ID}, going to assume that it supports C++11") + endif () + + ## TODO: Figure out how to detect this automatically -- GitLab From 9b309b74f1f46d709a6222cf1c1aedea53f08f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 15:35:02 +0200 Subject: [PATCH 1140/1172] drop libreadline dep, add ncurses in MySQL easyconfig --- .../m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb index d630176fd8..6104ea8d3a 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [ ('libevent', '2.0.22'), - ('libreadline', '6.3'), + ('ncurses', '5.9'), ('zlib', '1.2.8'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons ] -- GitLab From b83c961af4a9a494180f8eee43b70093145d2963 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 15:55:40 +0200 Subject: [PATCH 1141/1172] bump to Jellyfish 2.2.3 --- ...sh-2.2.0-intel-2015b.eb => Jellyfish-2.2.3-intel-2015b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/j/Jellyfish/{Jellyfish-2.2.0-intel-2015b.eb => Jellyfish-2.2.3-intel-2015b.eb} (87%) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb similarity index 87% rename from easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb rename to easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb index 504c9b0c81..04f8a538da 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb @@ -5,14 +5,14 @@ easyblock = 'ConfigureMake' name = 'Jellyfish' -version = '2.2.0' +version = '2.2.3' homepage = 'http://www.genome.umd.edu/jellyfish.html' description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] parallel = 1 -- GitLab From a5bf540b1267d93065ace762b5f96903654c7ad9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 15:57:41 +0200 Subject: [PATCH 1142/1172] remove unused easyconfigs --- .../c/CMake/CMake-3.3.2-foss-2015b.eb | 31 ------------------- .../easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 23 -------------- 2 files changed, 54 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb delete mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb deleted file mode 100644 index 9d27256dc6..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-foss-2015b.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.3.2' - -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': '2015b'} - -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/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb deleted file mode 100644 index b66775c7a6..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ /dev/null @@ -1,23 +0,0 @@ -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': 'foss', 'version': '2015b'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 7821898cdc7938c6251b0c3323aeb7df353e562b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 16:09:54 +0200 Subject: [PATCH 1143/1172] fix dev version to follow PEP-440, which setuptools basically jams down our throat --- setup.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5d2a2c7ab6..0d73c21edf 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,13 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.4.0dev' +# +# important note: dev versions should follow the 'X.Y.Z.dev0' format +# see https://www.python.org/dev/peps/pep-0440/#developmental-releases +# 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 = '2.4.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From ce1fa5a1218c89af8abfe92b87fadc33b15fd179 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 16:13:36 +0200 Subject: [PATCH 1144/1172] remove unused Bison easyconfig --- .../b/Bison/Bison-3.0.2-foss-2015b.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb deleted file mode 100644 index 7144e90187..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015b.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Bison' -version = '3.0.2' - -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': 'foss', 'version': '2015b'} - -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' -- GitLab From fbbd41703d5441777e897e7917d7d4381c29c344 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 16:36:56 +0200 Subject: [PATCH 1145/1172] don't use included Jellyfish in Sailfish --- ...ailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 5 ++- .../Sailfish-0.7.4_bypass-C++11-check.patch | 4 +-- ...ilfish-0.7.4_skip-included-Jellyfish.patch | 34 +++++++++++++++++++ 3 files changed, 40 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 198925231e..8f3fd4b8af 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['Sailfish-%(version)s_bypass-C++11-check.patch'] +patches = [ + 'Sailfish-%(version)s_bypass-C++11-check.patch', + 'Sailfish-%(version)s_skip-included-Jellyfish.patch', +] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch index b44441022a..3cb7d315e7 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch @@ -1,5 +1,5 @@ ---- CMakeLists.txt.orig 2015-09-25 14:52:46.821073663 +0200 -+++ CMakeLists.txt 2015-09-25 14:55:23.814696637 +0200 +--- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 @@ -119,7 +119,8 @@ set (PTHREAD_LIB "pthread") endif() diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch new file mode 100644 index 0000000000..be929fbe76 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch @@ -0,0 +1,34 @@ +--- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 +@@ -274,21 +275,6 @@ + + set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib) + +-message("Build system will fetch and build Jellyfish") +-message("==================================================================") +-ExternalProject_Add(libjellyfish +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix= CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_IN_SOURCE 1 +- INSTALL_COMMAND make install && +- cp config.h /include/jellyfish-2.1.3/jellyfish/ && +- cp config.h /include/ +-) +- + find_package(TBB) + ## + # +--- src/CMakeLists.txt.orig 2015-09-25 16:29:56.827724434 +0200 ++++ src/CMakeLists.txt 2015-09-25 16:30:01.347815059 +0200 +@@ -40,7 +40,6 @@ + ${GAT_SOURCE_DIR}/external/cereal/include + ${GAT_SOURCE_DIR}/external/install/include + ${GAT_SOURCE_DIR}/external/install/include/rapmap +-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.1.3 + ${ZLIB_INCLUDE_DIR} + ${TBB_INCLUDE_DIRS} + ${Boost_INCLUDE_DIRS} -- GitLab From 0e9c02a644890bc5b1879372594b8020afaa6838 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 16:43:38 +0200 Subject: [PATCH 1146/1172] add libedit dep + remove prebundled version --- .../easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb | 2 +- .../m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb index 3284f299e7..c56c34addf 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -24,7 +24,7 @@ builddependencies = [ ] # remove prebundled version of libedit -preconfigopts = "rm -rf cmd-line-utils && " +preconfigopts = "rm -rf cmd-line-utils/libedit && " configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" # do not use ld.gold diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb index 6104ea8d3a..9ff8823452 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} dependencies = [ ('libevent', '2.0.22'), ('ncurses', '5.9'), + ('libedit', '20150325'), ('zlib', '1.2.8'), # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons ] @@ -26,6 +27,9 @@ builddependencies = [ ('CMake', '3.3.2'), ] +# remove prebundled version of libedit +preconfigopts = "rm -rf cmd-line-utils/libedit && " + configopts = "-DWITHOUT_SERVER=ON " sanity_check_paths = { -- GitLab From 066232478c16be81974cfdfa047a8ff4216f9f19 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 25 Sep 2015 16:48:56 +0200 Subject: [PATCH 1147/1172] Remove dependency on GCC built dependencies --- .../Autotools-20150119-intel-2015a.eb | 18 +++++++++++++++ .../b/Bison/Bison-3.0.4-intel-2015a.eb | 23 +++++++++++++++++++ .../libpciaccess-0.13.1-intel-2015a.eb | 2 +- .../l/libtool/libtool-2.4.5-intel-2015a.eb | 18 +++++++++++++++ .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 15 ++++++------ .../xorg-macros-1.17-intel-2015a.eb | 2 +- 6 files changed, 68 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb new file mode 100644 index 0000000000..c792112632 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150119' # 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': '2015a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.5'), # 20150119 +] + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb new file mode 100644 index 0000000000..08d07fb3ba --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb @@ -0,0 +1,23 @@ +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': '2015a'} + +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/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index ce77f3502c..33bdd6c5c3 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 @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} builddependencies = [ - ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('Autotools', '20150119'), ('xorg-macros', '1.17'), ] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb new file mode 100644 index 0000000000..e0df416d77 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.5' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' + 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 9f2977a63e..30ec7a0f50 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 @@ -21,16 +21,16 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) builddependencies = [ - ('flex', '2.5.39', '', ('GCC', '4.9.2')), - ('Bison', '3.0.4', '', ('GCC', '4.9.2')), - ('Autotools', '20150119', '', ('GCC', '4.9.2')), - ('pkg-config', '0.28', '', ('GCC', '4.9.2')), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('Autotools', '20150119'), + ('pkg-config', '0.28'), ('glproto', '1.4.17'), ('kbproto', '1.0.6'), ('xextproto', '7.3.0'), ('xproto', '7.0.27'), ('makedepend', '1.0.5'), - ('M4', '1.4.17', '', ('GCC', '4.9.2')), + ('M4', '1.4.17'), ] dependencies = [ @@ -54,10 +54,9 @@ configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm -- configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --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="$EBROOTLIBDRM/include/libdrm" ' +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', @@ -69,6 +68,6 @@ sanity_check_paths = { 'dirs': [] } -maxparallel = 1 +#maxparallel = 1 moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb index 195ab46393..e392070fcf 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! sources = ['util-macros-%(version)s.tar.gz'] -dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +dependencies = [('Autotools', '20150119')] preconfigopts = './autogen.sh && ' -- GitLab From 517395e68bb98b2e7a5c8d1c62c4da3c9c1084ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:02:05 +0200 Subject: [PATCH 1148/1172] bump Jellyfish easyconfig, cp config.h for Jellyfish and set correct $CPATH --- .../easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb | 4 ++++ .../s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb index 04f8a538da..2bb091ce5a 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb @@ -20,9 +20,13 @@ parallel = 1 # The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense runtest = "check GTEST_FILTER=-'*Bloom*'" +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/"] + sanity_check_paths = { 'files': ['bin/jellyfish'], 'dirs': [] } +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 8f3fd4b8af..3ed0c155ae 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -28,7 +28,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), ('tbb', '4.3.6.211', '', True), - ('Jellyfish', '2.2.0'), + ('Jellyfish', '2.2.3'), ('g2log', '1.0'), ] -- GitLab From d83405191a90c0035dc67f6d69f01df0de1b942a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:03:13 +0200 Subject: [PATCH 1149/1172] specify -DWITH_EDITLINE=system in MySQL easyconfig --- .../m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb index 9ff8823452..bae1276ac2 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -27,10 +27,7 @@ builddependencies = [ ('CMake', '3.3.2'), ] -# remove prebundled version of libedit -preconfigopts = "rm -rf cmd-line-utils/libedit && " - -configopts = "-DWITHOUT_SERVER=ON " +configopts = "-DWITHOUT_SERVER=ON -DWITH_EDITLINE=system" sanity_check_paths = { 'files': ['bin/mysql'], -- GitLab From d80b2fb816b4383a6e8f36d72356a728b63854c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:08:04 +0200 Subject: [PATCH 1150/1172] correct location where config.h is copied to --- .../easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb index 2bb091ce5a..5e170ee4c5 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb @@ -20,7 +20,7 @@ parallel = 1 # The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense runtest = "check GTEST_FILTER=-'*Bloom*'" -postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/"] +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] sanity_check_paths = { 'files': ['bin/jellyfish'], -- GitLab From c6e70942720f63b53b7b1d4c513a63d13dff7671 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 25 Sep 2015 17:10:02 +0200 Subject: [PATCH 1151/1172] Add intel GMP build --- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 27 +++++++++++++++++++ .../p/Python/Python-2.7.10-intel-2015a.eb | 2 +- 2 files changed, 28 insertions(+), 1 deletion(-) 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..5e19c6ead0 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -0,0 +1,27 @@ +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': '2015.07'} +toolchainopts = {'optarch': True, 'pic': True, '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' + diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index f5c2309ea8..0f2e684636 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), - ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto + ('GMP', '6.0.0a',), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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 f10513691b438651611bd584955b298b699fb43b Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 25 Sep 2015 17:16:07 +0200 Subject: [PATCH 1152/1172] Typo --- 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 5e19c6ead0..514b540283 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 @@ -7,7 +7,7 @@ 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': 'intel', 'version': '2015.07'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'precise': True} sources = [SOURCELOWER_TAR_BZ2] -- GitLab From 61894fe404825760636d67498198691f5550b904 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:46:00 +0200 Subject: [PATCH 1153/1172] remove updating of $CMAKE_INCLUDE_PATH in Sailfish easyconfigs, no longer needed --- .../s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 1 - .../s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index b8fe958616..371c7d12e5 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -26,7 +26,6 @@ dependencies = [ ('g2log', '1.0'), ] -preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" parallel = 1 diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 3ed0c155ae..c80c41e1d5 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -32,7 +32,6 @@ dependencies = [ ('g2log', '1.0'), ] -preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" parallel = 1 -- GitLab From 0b7c4e1f5de3213d667a2dcdd0e2b942c71b9193 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:47:38 +0200 Subject: [PATCH 1154/1172] add comments to patch files --- .../s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch | 2 ++ .../s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch index 3cb7d315e7..223ee7d99d 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch @@ -1,3 +1,5 @@ +bypass C++11 compatibility check, since it's unaware of Intel compilers (onlt knows about GCC & Clang) +author: Kenneth Hoste (HPC-UGent) --- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 +++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 @@ -119,7 +119,8 @@ diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch index be929fbe76..19668e74c3 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch @@ -1,3 +1,5 @@ +remove fetching/building of Jellyfish, since it's provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) --- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 +++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 @@ -274,21 +275,6 @@ -- GitLab From 98785537bd4f5e53cec42170171020bb9153c712 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2015 17:59:51 +0200 Subject: [PATCH 1155/1172] fix determining suffix for API version --- setup.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 0d73c21edf..460e2b5145 100644 --- a/setup.py +++ b/setup.py @@ -57,9 +57,11 @@ rc_regexp = re.compile("^.*(rc[0-9]*)$") res = rc_regexp.search(str(VERSION)) if res: suff = res.group(1) -dev_regexp = re.compile("^.*[0-9]dev$") -if dev_regexp.match(VERSION): - suff = 'dev' + +dev_regexp = re.compile("^.*[0-9](.?dev[0-9])$") +res = dev_regexp.search(VERSION) +if res: + suff = res.group(1) API_VERSION += suff EB_VERSION += suff -- GitLab From 6af8bb480e062027c123fc0f59b25dd0a1079610 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2015 09:44:00 +0200 Subject: [PATCH 1156/1172] {bio}[intel/2015b] SAMtools 1.2 + HTSlib 1.2.1 --- .../h/HTSlib/HTSlib-1.2.1-intel-2015b.eb | 27 +++++++++++++ .../SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb | 38 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb new file mode 100644 index 0000000000..465b0a7d53 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.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 = '1.2.1' + +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': 'intel', 'version': '2015b'} + +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.so"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb new file mode 100644 index 0000000000..739c632246 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.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:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format""" + +toolchain = {'name': 'intel', 'version': '2015b'} +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'] + +htslib = 'HTSlib' +htsver = '1.2.1' +versionsuffix = '-%s-%s' % (htslib, htsver) + +dependencies = [ + (htslib, htsver), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' -- GitLab From 60fdbb4c3020efc827f64de6d2b2ee544be2f195 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2015 14:54:43 +0200 Subject: [PATCH 1157/1172] {bio}[dummy] SRA-Toolkit 2.5.4-1 --- .../SRA-Toolkit-2.5.4-1-centos_linux64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb new file mode 100644 index 0000000000..54156d4303 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb @@ -0,0 +1,26 @@ +# 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 = 'SRA-Toolkit' +version = '2.5.4-1' +versionsuffix = '-centos_linux64' + +homepage = 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std' +description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing files + from the SRA database and writing (loading) files into the .sra format """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["sra-stat", "sra-sort", "srapath", "bam-load"]], + 'dirs': ["example", "schema"], +} + +moduleclass = 'bio' -- GitLab From 876409063f0795f4819393d5b319d24290b8ea7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Mon, 28 Sep 2015 09:58:06 +0200 Subject: [PATCH 1158/1172] Revert "Mesa.10.5.5" --- .../Autotools-20150119-intel-2015a.eb | 18 ------------- .../b/Bison/Bison-3.0.4-intel-2015a.eb | 23 ---------------- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 27 ------------------- .../libpciaccess-0.13.1-intel-2015a.eb | 2 +- .../l/libtool/libtool-2.4.5-intel-2015a.eb | 18 ------------- .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 15 ++++++----- .../p/Python/Python-2.7.10-intel-2015a.eb | 2 +- .../xorg-macros-1.17-intel-2015a.eb | 2 +- 8 files changed, 11 insertions(+), 96 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb deleted file mode 100644 index c792112632..0000000000 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-intel-2015a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20150119' # 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': '2015a'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15'), # 20150105 - ('libtool', '2.4.5'), # 20150119 -] - -moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb deleted file mode 100644 index 08d07fb3ba..0000000000 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2015a.eb +++ /dev/null @@ -1,23 +0,0 @@ -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': '2015a'} - -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/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 514b540283..0000000000 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ /dev/null @@ -1,27 +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 = {'optarch': True, 'pic': True, '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' - 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 33bdd6c5c3..ce77f3502c 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 @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} builddependencies = [ - ('Autotools', '20150119'), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), ('xorg-macros', '1.17'), ] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb deleted file mode 100644 index e0df416d77..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-intel-2015a.eb +++ /dev/null @@ -1,18 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.5' - -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': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -dependencies = [('M4', '1.4.17')] - -moduleclass = 'lib' - 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 30ec7a0f50..9f2977a63e 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 @@ -21,16 +21,16 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.4'), - ('Autotools', '20150119'), - ('pkg-config', '0.28'), + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('pkg-config', '0.28', '', ('GCC', '4.9.2')), ('glproto', '1.4.17'), ('kbproto', '1.0.6'), ('xextproto', '7.3.0'), ('xproto', '7.0.27'), ('makedepend', '1.0.5'), - ('M4', '1.4.17'), + ('M4', '1.4.17', '', ('GCC', '4.9.2')), ] dependencies = [ @@ -54,9 +54,10 @@ configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm -- configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --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:$CPATH" ' +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' sanity_check_paths = { 'files': ['lib/libGL.so', 'lib/libOSMesa.so', @@ -68,6 +69,6 @@ sanity_check_paths = { 'dirs': [] } -#maxparallel = 1 +maxparallel = 1 moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 0f2e684636..f5c2309ea8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), - ('GMP', '6.0.0a',), # required for pycrypto + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto # ('OpenSSL', '1.0.1m'), # 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/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb index e392070fcf..195ab46393 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! sources = ['util-macros-%(version)s.tar.gz'] -dependencies = [('Autotools', '20150119')] +dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] preconfigopts = './autogen.sh && ' -- GitLab From caa6f5cc403a5f47b8efdf283354dbf04232b664 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 17:02:18 +0200 Subject: [PATCH 1159/1172] {numlib}[intel/2015b] Hypre 2.10.1 --- .../h/Hypre/Hypre-2.10.1-intel-2015b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb new file mode 100644 index 0000000000..aba4719bc9 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.10.1' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['https://computation.llnl.gov/project/linear_solvers/download/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' -- GitLab From fa6b5b2a1b17fecdbc900d25ec5e3ea28fddb627 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 17:55:41 +0200 Subject: [PATCH 1160/1172] {tools}[dummy] Aspera Connect 3.6.1 --- .../a/Aspera-Connect/Aspera-Connect-3.6.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb diff --git a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb new file mode 100644 index 0000000000..fcfb24eb69 --- /dev/null +++ b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'Binary' + +name = 'Aspera-Connect' +version = '3.6.1' + +homepage = 'http://downloads.asperasoft.com/connect2/' +description = """Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and + downloads with an Aspera transfer server.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://download.asperasoft.com/download/sw/connect/%(version)s/'] +sources = ['%(namelower)s-%(version)s.110647-linux-64.tar.gz'] + +install_cmd = "tar xfvz %(namelower)s*.tar.gz && HOME=%(builddir)s ./%(namelower)s*.sh && " +install_cmd += "cp -a %(builddir)s/.aspera/connect/* %(installdir)s" + +sanity_check_paths = { + 'files': ['bin/asperaconnect'], + 'dirs': ['lib'], +} + +moduleclass = 'tools' -- GitLab From 0f71c413a3ff082aca0680e93a1ae6879fbc3156 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 17:57:47 +0200 Subject: [PATCH 1161/1172] add clarifying comment --- easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb index fcfb24eb69..61380b292e 100644 --- a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb +++ b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://download.asperasoft.com/download/sw/connect/%(version)s/'] sources = ['%(namelower)s-%(version)s.110647-linux-64.tar.gz'] +# install script has ~/.aspera/connect hardcoded, but this can be overridden by redefining $HOME install_cmd = "tar xfvz %(namelower)s*.tar.gz && HOME=%(builddir)s ./%(namelower)s*.sh && " install_cmd += "cp -a %(builddir)s/.aspera/connect/* %(installdir)s" -- GitLab From 30c3ba1e367872c9acae2c32c2a9f599910fd81b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 18:09:07 +0200 Subject: [PATCH 1162/1172] flesh out sanity check for Aspera Connect --- easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb index 61380b292e..d5fdd13376 100644 --- a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb +++ b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb @@ -17,7 +17,7 @@ install_cmd = "tar xfvz %(namelower)s*.tar.gz && HOME=%(builddir)s ./%(namelower install_cmd += "cp -a %(builddir)s/.aspera/connect/* %(installdir)s" sanity_check_paths = { - 'files': ['bin/asperaconnect'], + 'files': ['bin/%s' % x for x in ['ascp', 'asperaconnect', 'asperaconnect.bin', 'asperacrypt', 'asunprotect']], 'dirs': ['lib'], } -- GitLab From 970fc73b9d66bbea24c8ae95aef25d36312c852d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 18:56:05 +0200 Subject: [PATCH 1163/1172] {lang}[intel/2015b] Python 3.5.0 + several pkgs on top of it --- ...tplotlib-1.4.3-intel-2015b-Python-3.5.0.eb | 37 ++++++ .../networkx-1.10-intel-2015b-Python-3.5.0.eb | 29 +++++ .../Pillow-2.9.0-intel-2015b-Python-3.5.0.eb | 23 ++++ .../p/Python/Python-3.4.3-intel-2015a.eb | 2 + .../p/Python/Python-3.5.0-intel-2015b.eb | 115 ++++++++++++++++++ ...t-image-0.11.3-intel-2015b-Python-3.5.0.eb | 38 ++++++ ...t-learn-0.16.1-intel-2015b-Python-3.5.0.eb | 34 ++++++ 7 files changed, 278 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000..741df4d0ff --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib' +version = '1.4.3' + +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': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = 'Python' +pythonversion = '3.5.0' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000..089cc6d27d --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000..9e482ed565 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.9.0' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 1aa8ae3172..5741325e74 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -111,3 +111,5 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb new file mode 100644 index 0000000000..088e6f96d9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '3.5.0' + +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': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.3' +scipyversion = '0.16.0' + +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', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1p'), # 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')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '18.3.2', { + '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': ['https://pypi.python.org/packages/source/n/numpy/'], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + }), + ('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/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.0', { + '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', '0.23.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + '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/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('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', '1.15.2', { + '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', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000..6d4468286e --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.11.3' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('Qhull', '2012.1'), + ('matplotlib', '1.4.3', versionsuffix), + ('networkx', '1.10', versionsuffix), + ('Pillow', '2.9.0', versionsuffix), +] + +options = {'modulename': 'skimage'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +pylibdir = 'lib/python%s/site-packages' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': ['%s/scikit_image-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000..27c24dc20d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +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': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} + +moduleclass = 'data' -- GitLab From 086d9b2e633930a06c578dc6fed7aab705560f38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Sep 2015 19:20:45 +0200 Subject: [PATCH 1164/1172] {vis}[intel/2015b] animation 2.4 (R v3.2.1) + GraphicsMagick 1.3.21 + ffmpeg 2.8 --- .../animation-2.4-intel-2015b-R-3.2.1.eb | 32 +++++++++++++++++++ .../f/ffmpeg/ffmpeg-2.8-intel-2015b.eb | 28 ++++++++++++++++ .../GraphicsMagick-1.3.21-intel-2015b.eb | 19 +++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb create mode 100644 easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb diff --git a/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb new file mode 100644 index 0000000000..9260cfb552 --- /dev/null +++ b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'animation' +version = '2.4' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """animation: A Gallery of Animations in Statistics and Utilities to Create Animations""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.2.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('ffmpeg', '2.8'), + ('GraphicsMagick', '1.3.21'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['animation'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb new file mode 100644 index 0000000000..84c4dd1f59 --- /dev/null +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ffmpeg' +version = '2.8' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), +] + +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' 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 new file mode 100644 index 0000000000..79af50f760 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.21' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +runtest = 'check' + +moduleclass = 'vis' -- GitLab From f20867a5fbf6005900363d7411639c0e95cb70fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2015 09:02:10 +0200 Subject: [PATCH 1165/1172] don't run 'make check' for GraphicsMagic, it hangs? --- .../g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb | 2 -- 1 file changed, 2 deletions(-) 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 79af50f760..513feabb7e 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 @@ -14,6 +14,4 @@ source_urls = [ ] sources = [SOURCE_TAR_GZ] -runtest = 'check' - moduleclass = 'vis' -- GitLab From 0078ea07bfc5b4751af7328dbd22c034316e1236 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2015 10:54:08 +0200 Subject: [PATCH 1166/1172] lxml-3.4.2 intel-2014b --- .../l/libxslt/libxslt-1.1.28-intel-2014b.eb | 24 +++++++++++++ .../lxml-3.4.2-intel-2014b-Python-2.7.8.eb | 34 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb new file mode 100644 index 0000000000..f2bb78109e --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.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': '2014b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.1'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..af8b151071 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'lxml' +version = '3.4.2' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +python = 'Python' +pythonversion = '2.7.8' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libxml2', '2.9.1'), + ('libxslt', '1.1.28'), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'lib' -- GitLab From 6f55300292adf130998bd24fa19ec3925f00d70e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2015 11:08:41 +0200 Subject: [PATCH 1167/1172] {vis} [intel-2014b] PyQt 4.11.4 (REVIEW) --- .../PyQt-4.11.4-intel-2014b-Python-2.7.8.eb | 41 +++++++++++++++++++ .../SIP-4.16.8-intel-2014b-Python-2.7.8.eb | 33 +++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..0d39a830f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..d266d5f8e0 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From e9ca0a7a298a4d2449cacf6971fe34dc1208b779 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2015 13:49:28 +0200 Subject: [PATCH 1168/1172] {data} [intel-2014b] MySQLdb 1.2.5 Python 2.7.8 (REVIEW) --- .../MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..37c343509e --- /dev/null +++ b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'MySQLdb' +version = '1.2.5' + +homepage = [ + 'http://mysql-python.sourceforge.net/', + 'https://pypi.python.org/pypi/MySQL-python/', +] + +description = """MySQLdb is an interface to the popular MySQL database server for Python.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/M/MySQL-python/'] +sources = ['MySQL-python-%(version)s.zip'] +checksums = ['654f75b302db6ed8dc5a898c625e030c'] + +python = 'Python' +pythonversion = '2.7.8' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('MySQL', '5.6.20', '-clientonly'), +] + +options = {'modulename': '%(name)s'} + +pylibdir = "lib/python%s/site-packages/MySQL_python" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'data' -- GitLab From 553b2a9550e666c4e2efaf8ab4173dbdcf4e4f3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2015 13:57:15 +0200 Subject: [PATCH 1169/1172] libxml2 2.9.1 -> 2.9.2 --- easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb | 2 +- .../easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb index f2bb78109e..da4b7d1bbd 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('zlib', '1.2.8'), - ('libxml2', '2.9.1'), + ('libxml2', '2.9.2'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb index af8b151071..c64a9a648d 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('libxml2', '2.9.1'), + ('libxml2', '2.9.2'), ('libxslt', '1.1.28'), ] -- GitLab From de5b9256f850969af66cc1fae047f60208d25533 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2015 14:12:34 +0200 Subject: [PATCH 1170/1172] only one homepage --- .../m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb index 37c343509e..93f03d3fd4 100644 --- a/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb @@ -3,10 +3,7 @@ easyblock = "PythonPackage" name = 'MySQLdb' version = '1.2.5' -homepage = [ - 'http://mysql-python.sourceforge.net/', - 'https://pypi.python.org/pypi/MySQL-python/', -] +homepage = 'https://pypi.python.org/pypi/MySQL-python/' description = """MySQLdb is an interface to the popular MySQL database server for Python.""" -- GitLab From 912490bd138c52a337496fb3582a843b7517648e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2015 14:19:20 +0200 Subject: [PATCH 1171/1172] fix Sailfish 0.7.4 patch --- .../Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 2 +- .../Sailfish-0.7.4_skip-included-Jellyfish.patch | 12 ++++++++++-- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index 371c7d12e5..b503f4c639 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -29,5 +29,5 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" parallel = 1 -moduleclass = 'bio' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch index 19668e74c3..a47f914bc5 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch @@ -24,8 +24,8 @@ author: Kenneth Hoste (HPC-UGent) find_package(TBB) ## # ---- src/CMakeLists.txt.orig 2015-09-25 16:29:56.827724434 +0200 -+++ src/CMakeLists.txt 2015-09-25 16:30:01.347815059 +0200 +--- src/CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ src/CMakeLists.txt 2015-09-29 14:10:00.134610574 +0200 @@ -40,7 +40,6 @@ ${GAT_SOURCE_DIR}/external/cereal/include ${GAT_SOURCE_DIR}/external/install/include @@ -34,3 +34,11 @@ author: Kenneth Hoste (HPC-UGent) ${ZLIB_INCLUDE_DIR} ${TBB_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS} +@@ -85,7 +84,6 @@ + ${Boost_LIBRARIES} + gff + ${ZLIB_LIBRARY} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + m + ${TBB_LIBRARIES} + ${LIBSAILFISH_LINKER_FLAGS} -- GitLab From 27770219ae0464a2c347d6a473e35137c4f4c91e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Sep 2015 09:38:36 +0200 Subject: [PATCH 1172/1172] {chem}[intel/2015b] CHARMM 37b2 --- .../c/CHARMM/CHARMM-37b2-intel-2015b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb new file mode 100644 index 0000000000..417f7a8785 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = 'CHARMM' +version = '37b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' -- GitLab