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30
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# ABINIT recipe
# 2015 Martin Stachon <martin.stachon@vsb.cz>
##
easyblock = "ConfigureMake"
name = 'ABINIT'
version = '7.10.1'
homepage = 'http://www.abinit.org/'
description = """Abinit is a plane wave pseudopotential code for doing
condensed phase electronic structure calculations using DFT."""
toolchain = {'name': 'foss', 'version': '2015b'}
# eg. http://ftp.abinit.org/abinit-7.10.1.tar.gz
sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
source_urls = ['http://ftp.abinit.org/']
# sanity_check_paths = {
# 'files': ["bin/abinit"],
# 'dirs': []
# }
moduleclass = 'chem'
configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
''' --enable-debug="no" ''' + \
''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''

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name = 'ADF'
version = '2014.11.r48287'
homepage = 'http://www.scm.com/ADF/'
description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
predict chemical structure and reactivity with density functional theory (DFT)."""
toolchain = {'name': 'intel', 'version': '2016a'}
sources = [
'%(namelower)s%(version)s.src.tgz',
# no exact match on revision ID available, but not strictly needed
'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz',
]
license_file = HOME + "/licenses/ADF/license.txt"
modloadmsg = "These environment variables need to be defined before using ADF:\n"
modloadmsg += " * $SCMLICENSE: path to ADF license file\n"
modloadmsg += " * $SCM_TMPDIR: path to user scratch directory"
moduleclass = 'chem'

40
archive/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb Normal file
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easyblock = 'CMakeMake'
name = 'ALPS'
version = '2.3.0'
versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
C++ libraries for simplifying the development of such code.
"""
toolchain = {'name': 'foss', 'version': '2016b'}
toolchainopts = {'cstd': 'c++03'}
sources = ['%(namelower)s-%(version)s-src.tar.gz']
source_urls = ['http://alps.comp-phys.org/static/software/releases/']
dependencies = [
('CMake', '3.6.2'),
('Python', '2.7.12'),
('Boost', '1.63.0', versionsuffix),
('HDF5', '1.8.17')
]
separate_build_dir = True
modextravars = {
'ALPS_ROOT': '$root',
}
modextrapaths = {
'PYTHONPATH': ['lib/']
}
sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'],
}
moduleclass = 'phys'

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easyblock = 'CMakeMake'
name = 'ALPS'
version = '2.3.0'
versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
C++ libraries for simplifying the development of such code.
"""
toolchain = {'name': 'foss', 'version': '2016b'}
toolchainopts = {'cstd': 'c++03'}
sources = ['%(namelower)s-%(version)s-src.tar.gz']
source_urls = ['http://alps.comp-phys.org/static/software/releases/']
dependencies = [
('CMake', '3.6.2'),
('Python', '3.5.2'),
('Boost', '1.63.0', versionsuffix),
('HDF5', '1.8.17')
]
separate_build_dir = True
modextravars = {
'ALPS_ROOT': '$root',
}
modextrapaths = {
'PYTHONPATH': ['lib/']
}
sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'],
}
moduleclass = 'phys'

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#
# modified by Stephane Thiell (Stanford University) for Amber v14
#
# author: Benjamin P. Roberts (University of Auckland)
#
# based on work by Marios Constantinou (University of Cyprus)
#
easyblock = 'ConfigureMake'
name = 'AmberTools'
version = '14'
homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy
Refinement) is software for performing molecular dynamics and structure
prediction."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '15'
sources = [
# 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
configopts = '--no-updates'
# patches = [
# 'Amber-%(version)s_fix-hardcoding.patch',
# 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
#]
dependencies = [
# ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
patchlevels = (13, 13)
patchruns = 1
versionsuffix = '-Python-2.7.11)'
moduleclass = 'chem'

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easyblock = 'ConfigureMake'
name = 'AmberTools'
version = '16'
homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy
Refinement) is software for performing molecular dynamics and structure
prediction."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '16'
sources = [
# 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
patches = [
# 'Amber-%(version)s_fix-hardcoding.patch',
'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
]
dependencies = [
# ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
patchlevels = (13, 13)
patchruns = 1
versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (
ambertools_ver, patchlevels[0], patchlevels[1])
moduleclass = 'chem'

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name = 'Armadillo'
version = '7.500.0'
versionsuffix = '-Python-3.5.2'
homepage = 'http://arma.sourceforge.net/'
description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
as well as a subset of trigonometric and statistics functions."""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = [SOURCELOWER_TAR_XZ]
source_urls = ['http://sourceforge.net/projects/arma/files']
dependencies = [
('Boost', '1.61.0', '-serial'),
('arpack-ng', '3.3.0'),
('CMake', '3.5.2'),
('HDF5', '1.8.16'),
('libxml2', '2.9.3'),
('XZ', '5.2.2'),
]
moduleclass = 'numlib'

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easyblock = 'MakeCp'
name = 'angsd'
version = '0.910'
homepage = 'http://www.popgen.dk/angsd'
description = """Program for analysing NGS data."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['https://github.com/ANGSD/angsd/archive/']
sources = ['%(version)s.tar.gz']
dependencies = [('HTSlib', '1.3.1')]
files_to_copy = [
(['angsd'], 'bin'),
'doc',
]
sanity_check_paths = {
'files': ['bin/angsd'],
'dirs': ['doc'],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('foss', '2016a'))]
preconfigopts = "sh bootstrap && "
configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.so"],
'dirs': []
}
moduleclass = 'numlib'

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easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
# IT4I modification: because we have GCC 5.1.0 in intel/2015b toolchain...
builddependencies = [('Autotools', '20150215', '', ('GNU', '5.1.0-2.25'))]
preconfigopts = "sh bootstrap && "
configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.so"],
'dirs': []
}
moduleclass = 'numlib'

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easyblock = 'MakeCp'
name = 'BBMap'
version = '35.82'
homepage = 'https://sourceforge.net/projects/bbmap/'
description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'foss', 'version': '2015b'}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz']
java = 'Java'
javaver = '1.8.0_66'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver, '', True)]
prebuildopts = 'cd jni && '
suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
files_to_copy = ['*']
sanity_check_paths = {
'files': ['bbmap.sh'],
'dirs': []
}
modextrapaths = {'PATH': ''}
modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the
compiled jni C code."""
moduleclass = 'bio'

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easyblock = 'MakeCp'
name = 'BBMap'
version = '35.82'
homepage = 'https://sourceforge.net/projects/bbmap/'
description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'foss', 'version': '2015b'}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz']
java = 'Java'
javaver = '1.8.0_74'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver, '', True)]
prebuildopts = 'cd jni && '
suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
files_to_copy = ['*']
sanity_check_paths = {
'files': ['bbmap.sh'],
'dirs': []
}
modextrapaths = {'PATH': ''}
modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the
compiled jni C code."""
moduleclass = 'bio'

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easyblock = 'MakeCp'
name = 'BBMap'
version = '36.62'
versionsuffix = '-Java-%(javaver)s'
homepage = 'https://sourceforge.net/projects/bbmap/'
description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz']
dependencies = [('Java', '1.8.0_112', '', True)]
prebuildopts = 'cd jni && '
suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
files_to_copy = ['*']
sanity_check_paths = {
'files': ['bbmap.sh'],
'dirs': []
}
modextrapaths = {'PATH': ''}
modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the"
modloadmsg += " compiled jni C code.\n"
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.2'
homepage = 'http://www.htslib.org/'
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
dependencies = [
('HTSlib', '1.2.1'),
('zlib', '1.2.8'),
]
parallel = 1
skipsteps = ['configure']
installopts = ' prefix=%(installdir)s'
postinstallcmds = [
'mkdir -p %(installdir)s/lib/plugins',
'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
]
sanity_check_paths = {
'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.2'
homepage = 'http://www.htslib.org/'
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
dependencies = [
('HTSlib', '1.2.1'),
('zlib', '1.2.8'),
]
parallel = 1
skipsteps = ['configure']
installopts = ' prefix=%(installdir)s'
postinstallcmds = [
'mkdir -p %(installdir)s/lib/plugins',
'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
]
sanity_check_paths = {
'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.3'
homepage = 'http://www.htslib.org/'
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
toolchain = {'name': 'foss', 'version': '2015g'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
dependencies = [
('HTSlib', '1.3'),
('zlib', '1.2.8'),
]
parallel = 1
skipsteps = ['configure']
installopts = ' prefix=%(installdir)s'
postinstallcmds = [
'mkdir -p %(installdir)s/lib/plugins',
'cp plugins/*.so %(installdir)s/lib/plugins/.',
]
sanity_check_paths = {
'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.3'
homepage = 'http://www.htslib.org/'
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
dependencies = [
('HTSlib', '1.3'),
('zlib', '1.2.8'),
('GSL', '2.1'),
]
parallel = 1
skipsteps = ['configure']
buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1'
installopts = ' prefix=%(installdir)s'
postinstallcmds = [
'mkdir -p %(installdir)s/lib/plugins',
'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
]
sanity_check_paths = {
'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.3'
homepage = 'http://www.htslib.org/'
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
dependencies = [
('zlib', '1.2.8'),
('HTSlib', '1.3'),
('GSL', '2.1'),
]
parallel = 1
skipsteps = ['configure']
buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1'
installopts = ' prefix=%(installdir)s'
postinstallcmds = [
'mkdir -p %(installdir)s/lib/plugins',
'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
]
sanity_check_paths = {
'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'],
}
moduleclass = 'bio'

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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Author: Adam Huffman
# adam.huffman@crick.ac.uk
# The Francis Crick Institute
#
# This is the version with the bundled libStatGen library
name = 'BamUtil'
version = '1.0.13'
easyblock = 'MakeCp'
homepage = 'http://genome.sph.umich.edu/wiki/BamUtil'
description = """BamUtil is a repository that contains several programs
that perform operations on SAM/BAM files. All of these programs
are built into a single executable, bam."""
toolchain = {'name': 'foss', 'version': '2015b'}
sources = ['%(name)sLibStatGen.%(version)s.tgz']
source_urls = ['http://genome.sph.umich.edu/w/images/7/70/']
files_to_copy = ["bamUtil/bin", "libStatGen"]
sanity_check_paths = {
'files': ["bin/bam"],
'dirs': ["libStatGen"],
}
moduleclass = 'bio'

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##
# 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 <valentin.plugaru@gmail.com>
# 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 = 'Bash'
version = '4.2'
homepage = 'http://www.gnu.org/software/bash'
description = """Bash is an sh-compatible command language interpreter that executes commands
read from the standard input or from a file. Bash also incorporates useful features from the
Korn and C shells (ksh and csh)."""
toolchain = {'name': 'intel', 'version': '2015b'}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [GNU_SOURCE]
sanity_check_paths = {
'files': ["bin/bash"],
'dirs': []
}
moduleclass = 'tools'

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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp'
name = 'BayeScEnv'
version = '1.1'
homepage = 'https://github.com/devillemereuil/bayescenv'
description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect
local adaptation."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'openmp': True}
source_urls = ['https://github.com/devillemereuil/bayescenv/archive/']
sources = ['v%(version)s.tar.gz']
start_dir = 'source'
files_to_copy = [(['source/bayescenv'], 'bin'), 'test',
'COPYING', 'README.md', 'ChangeLog']
parallel = 1
sanity_check_paths = {
'files': ['bin/bayescenv'],
'dirs': [],
}
moduleclass = 'bio'

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@ -0,0 +1,39 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp'
name = 'BayeScan'
version = '2.1'
homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
using differences in allele frequencies between populations."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'openmp': True}
source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/']
sources = ['%(name)s%(version)s.zip']
prebuildopts = "sed -i.bk 's/g++/${CXX} ${CXXFLAGS}/g' Makefile && "
start_dir = 'source'
files_to_copy = [
(['source/bayescan_%(version)s'], 'bin'),
'BayeScan%(version)s_manual.pdf',
'input_examples',
'R functions'
]
parallel = 1
sanity_check_paths = {
'files': ['bin/bayescan_%(version)s'],
'dirs': [],
}
moduleclass = 'bio'

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easyblock = 'ConfigureMake'
name = 'BayesAss'
version = '3.0.4'
homepage = 'http://www.rannala.org/?page_id=245'
description = """
BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
"""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = ['BA3-%(version)s.tar.gz']
source_urls = [
'http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/']
dependencies = [
('GSL', '2.1')
]
runtest = 'check'
sanity_check_paths = {
'files': ['bin/BA3'],
'dirs': ['bin', 'include']
}
moduleclass = 'bio'

37
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@ -0,0 +1,37 @@
easyblock = 'ConfigureMake'
name = 'BerkeleyGW'
version = "1.0.6"
homepage = 'http://www.berkeleygw.org'
description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
properties and the optical responses of a large variety of materials from bulk periodic crystals to
nanostructures such as slabs, wires and molecules."""
toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
toolchainopts = {'usempi': True}
source_urls = ['http://www.berkeleygw.org/releases/']
sources = ['BGW-%(version)s.tar.gz']
checksums = ['8740562da41e87a62eb8d457675e4bfd']
skipsteps = ['configure']
prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && '
buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" '
buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" '
buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" '
buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" '
buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" '
installopts = 'INSTDIR=%(installdir)s'
sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']],
'dirs': []
}
moduleclass = 'phys'

37
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@ -0,0 +1,37 @@
easyblock = 'ConfigureMake'
name = 'BerkeleyGW'
version = "1.1-beta2"
homepage = 'http://www.berkeleygw.org'
description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
properties and the optical responses of a large variety of materials from bulk periodic crystals to
nanostructures such as slabs, wires and molecules."""
toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
toolchainopts = {'usempi': True}
source_urls = ['http://www.berkeleygw.org/releases/']
sources = ['BGW-%(version)s.tar.gz']
checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2']
skipsteps = ['configure']
prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && '
buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" '
buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" '
buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" '
buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" '
buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" '
installopts = 'INSTDIR=%(installdir)s'
sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']],
'dirs': []
}
moduleclass = 'phys'

39
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@ -0,0 +1,39 @@
easyblock = 'Bundle'
name = 'BioPerl'
version = '1.6.924'
versionsuffix = '-Perl-%(perlver)s'
homepage = 'http://www.bioperl.org/'
description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
Examples include Sequence objects, Alignment objects and database searching objects."""
toolchain = {'name': 'foss', 'version': '2016a'}
# this is a bundle of Perl modules
exts_defaultclass = 'PerlModule'
exts_filter = ("perldoc -lm %(ext_name)s ", "")
dependencies = [
('Perl', '5.22.1'),
('DB_File', '1.835', versionsuffix),
]
exts_list = [
# CGI has been removed from the Perl core since version 5.22
('CGI', '4.28', {
'source_tmpl': 'CGI-4.28.tar.gz',
'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'],
}),
(name, version, {
'modulename': 'Bio::Perl',
'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'),
'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'],
}),
]
modextrapaths = {
'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'
}
moduleclass = 'bio'

38
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@ -0,0 +1,38 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 The Cyprus Institute
# Authors:: Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
#
##
easyblock = "PythonPackage"
name = 'Biopython'
version = '1.65'
versionsuffix = "-Python-%(pyver)s"
homepage = 'http://www.biopython.org'
description = """Biopython is a set of freely available tools for biological computation written
in Python by an international team of developers. It is a distributed collaborative effort to
develop Python libraries and applications which address the needs of current and future work in
bioinformatics. """
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['http://biopython.org/DIST']
sources = ['%(namelower)s-%(version)s.tar.gz']
dependencies = [
('Python', '2.7.11')
]
sanity_check_paths = {
'files': [],
'dirs': [
'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'}
moduleclass = 'bio'

42
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@ -0,0 +1,42 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 The Cyprus Institute
# Authors:: Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
#
##
# foss-2016b modified by:
# Adam Huffman
# The Francis Crick Institute
easyblock = "PythonPackage"
name = 'Biopython'
version = '1.68'
versionsuffix = "-Python-%(pyver)s"
homepage = 'http://www.biopython.org'
description = """Biopython is a set of freely available tools for biological computation written
in Python by an international team of developers. It is a distributed collaborative effort to
develop Python libraries and applications which address the needs of current and future work in
bioinformatics. """
toolchain = {'name': 'foss', 'version': '2016b'}
source_urls = ['http://biopython.org/DIST']
sources = ['%(namelower)s-%(version)s.tar.gz']
dependencies = [
('Python', '2.7.12')
]
sanity_check_paths = {
'files': [],
'dirs': [
'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'}
moduleclass = 'bio'

38
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@ -0,0 +1,38 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 The Cyprus Institute
# Authors:: Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
#
##
easyblock = 'PythonPackage'
name = 'Biopython'
version = '1.68'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.biopython.org'
description = """Biopython is a set of freely available tools for biological computation written
in Python by an international team of developers. It is a distributed collaborative effort to
develop Python libraries and applications which address the needs of current and future work in
bioinformatics. """
toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = ['http://biopython.org/DIST']
sources = [SOURCELOWER_TAR_GZ]
dependencies = [
('Python', '2.7.12')
]
sanity_check_paths = {
'files': [],
'dirs': [
'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'}
moduleclass = 'bio'

38
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@ -0,0 +1,38 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 The Cyprus Institute
# Authors:: Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
#
##
easyblock = 'PythonPackage'
name = 'Biopython'
version = '1.68'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.biopython.org'
description = """Biopython is a set of freely available tools for biological computation written
in Python by an international team of developers. It is a distributed collaborative effort to
develop Python libraries and applications which address the needs of current and future work in
bioinformatics. """
toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = ['http://biopython.org/DIST']
sources = [SOURCELOWER_TAR_GZ]
dependencies = [
('Python', '3.5.2')
]
sanity_check_paths = {
'files': [],
'dirs': [
'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'}
moduleclass = 'bio'

26
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@ -0,0 +1,26 @@
# Built with EasyBuild version 2.1.1 on 2015-08-10_13-26-38
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': '2015g'}
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'

25
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@ -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 = '2.7.9'
versionsuffix = '-Python-%s' % pythonversion
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', pythonversion),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
source_urls = [SOURCEFORGE_SOURCE]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2015b'}
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'

26
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@ -0,0 +1,26 @@
# Built with EasyBuild version 2.1.1 on 2015-08-10_13-26-38
name = 'Boost'
version = '1.60.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2015g'}
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'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.11'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
archive/b/Boost/Boost-1.60.0-foss-2016a.eb Normal file
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
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'

23
archive/b/Boost/Boost-1.60.0-intel-2015b-Python-2.7.11.eb Normal file
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.11'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
archive/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb Normal file
View File

@ -0,0 +1,23 @@
name = 'Boost'
version = '1.60.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.11'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

21
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@ -0,0 +1,21 @@
name = 'Boost'
version = '1.60.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.61.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '3.5.2'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

25
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@ -0,0 +1,25 @@
name = 'Boost'
version = '1.61.0'
versionsuffix = '-serial'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
configopts = '--with-libraries=serialization'
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.61.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.61.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.11'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

21
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@ -0,0 +1,21 @@
name = 'Boost'
version = '1.61.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
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View File

@ -0,0 +1,23 @@
name = 'Boost'
version = '1.61.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016b'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.12'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
archive/b/Boost/Boost-1.61.0-intel-2016b.eb Normal file
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@ -0,0 +1,23 @@
name = 'Boost'
version = '1.61.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016b'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

23
archive/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb Normal file
View File

@ -0,0 +1,23 @@
name = 'Boost'
version = '1.62.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2016b'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', '2.7.12'),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

27
archive/b/Boost/Boost-1.63.0-foss-2015g-Python-3.6.1.eb Normal file
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@ -0,0 +1,27 @@
name = 'Boost'
version = '1.63.0'
versionsuffix = '-Python-%(pyver)s'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2015g'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
patches = [
'Boost-%(version)s_python3.patch',
]
dependencies = [
('bzip2', '1.0.6', '', True),
('zlib', '1.2.11', '', True),
('Python', '3.6.1', '', True),
]
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

28
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@ -0,0 +1,28 @@
name = 'Boost'
version = '1.63.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
pythonversion = '2.7.13'
versionsuffix = '-Python-%s' % pythonversion
dependencies = [
('bzip2', '1.0.6', '', True),
('zlib', '1.2.11', '', True),
('Python', pythonversion, '', True)
]
configopts = '--with-python=$EBROOTPYTHON/bin/python'
buildopts = '-fPIC &&'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'

55
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@ -0,0 +1,55 @@
# 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 <rjeschmi@gmail.com>
# 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'

55
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View File

@ -0,0 +1,55 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.6'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'foss', 'version': '2015b'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

55
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View File

@ -0,0 +1,55 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.6'
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': '2015b'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

57
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View File

@ -0,0 +1,57 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
# Modified by: Adam Huffman <adam.huffman@crick.ac.uk>
# The Francis Crick Institute
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.7'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'foss', 'version': '2015b'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

57
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View File

@ -0,0 +1,57 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
# Modified by: Adam Huffman <adam.huffman@crick.ac.uk>
# The Francis Crick Institute
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.8'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'foss', 'version': '2015b'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

57
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View File

@ -0,0 +1,57 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
# Modified by: Adam Huffman <adam.huffman@crick.ac.uk>
# The Francis Crick Institute
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.8'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

57
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View File

@ -0,0 +1,57 @@
# 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 <rjeschmi@gmail.com>
# Ottawa Hospital Research Institute - Bioinformatics Team
# Modified by: Adam Huffman <adam.huffman@crick.ac.uk>
# The Francis Crick Institute
easyblock = 'MakeCp'
name = 'Bowtie2'
version = '2.2.9'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [(["bowtie2",
"bowtie2-align-l",
"bowtie2-align-s",
"bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts",
"MANUAL",
"MANUAL.markdown",
"NEWS"]
sanity_check_paths = {
'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [],
}
# to add script folder to path just uncomment this line
#modextrapaths = {'PATH': 'scripts'}
moduleclass = 'bio'

32
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View File

@ -0,0 +1,32 @@
easyblock = 'CMakeMake'
name = 'Bullet'
version = '2.83.7'
homepage = "http://bulletphysics.org/"
description = """Bullet professional 3D Game Multiphysics Library provides state
of the art collision detection, soft body and rigid body dynamics."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'usempi': False, 'pic': True}
source_urls = ['https://github.com/bulletphysics/bullet3/archive/']
sources = ["%(version)s.tar.gz"]
builddependencies = [('CMake', '3.5.2')]
# build shared libraries
configopts = "-DBUILD_SHARED_LIBS=ON"
sanity_check_paths = {
'files': [
'include/bullet/btBullet%sCommon.h' %
x for x in [
'Collision', 'Dynamics']] + [
'lib/libBullet%s.%s' %
(x, SHLIB_EXT) for x in [
'Collision', 'Dynamics']], 'dirs': [], }
modextrapaths = {'CPATH': 'include/bullet'}
moduleclass = 'phys'

32
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@ -0,0 +1,32 @@
easyblock = 'CMakeMake'
name = 'Bullet'
version = '2.83.7'
homepage = "http://bulletphysics.org/"
description = """Bullet professional 3D Game Multiphysics Library provides state
of the art collision detection, soft body and rigid body dynamics."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'usempi': False, 'pic': True}
source_urls = ['https://github.com/bulletphysics/bullet3/archive/']
sources = ["%(version)s.tar.gz"]
builddependencies = [('CMake', '3.5.2')]
# build shared libraries
configopts = "-DBUILD_SHARED_LIBS=ON"
sanity_check_paths = {
'files': [
'include/bullet/btBullet%sCommon.h' %
x for x in [
'Collision', 'Dynamics']] + [
'lib/libBullet%s.%s' %
(x, SHLIB_EXT) for x in [
'Collision', 'Dynamics']], 'dirs': [], }
modextrapaths = {'CPATH': 'include/bullet'}
moduleclass = 'phys'

35
archive/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb Normal file
View File

@ -0,0 +1,35 @@
easyblock = 'ConfigureMake'
name = 'beagle-lib'
version = '2.1.2'
homepage = 'https://github.com/beagle-dev/beagle-lib'
description = """
beagle-lib is a high-performance library that can perform the core
calculations at the heart of most Bayesian and Maximum Likelihood
phylogenetics packages.
"""
toolchain = {'name': 'foss', 'version': '2016a'}
# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz
source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/']
sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')]
dependencies = [('Java', '1.8.0_74', '', True)]
builddependencies = [('Autotools', '20150215')]
# parallel build does not work (to test)
parallel = 1
preconfigopts = "./autogen.sh && "
sanity_check_paths = {
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile
for includefile in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % libfile
for libfile in ["-cpu", "-cpu-sse", "-jni", ""]],
'dirs': []
}
moduleclass = 'numlib'

36
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@ -0,0 +1,36 @@
easyblock = 'ConfigureMake'
name = 'beagle-lib'
# revision r1261
version = '20141202'
homepage = 'http://code.google.com/p/beagle-lib/'
description = """beagle-lib is a high-performance library that can perform the core
calculations at the heart of most Bayesian and Maximum Likelihood
phylogenetics packages."""
toolchain = {'name': 'intel', 'version': '2015a'}
# there is no tarball provided, only SVN checkout through:
# svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib
sources = [SOURCE_TGZ]
dependencies = [
('Java', '1.8.0_31', '', True),
('Autoconf', '2.69')
]
preconfigopts = './autogen.sh && '
# parallel build does not work
parallel = 1
sanity_check_paths = {
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile
for includefile in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % libfile
for libfile in ["-cpu", "-cpu-sse", "-jni", ""]],
'dirs': []
}
moduleclass = 'numlib'

37
archive/c/CASMcode/CASMcode-0.2.1-foss-2016a-Python-2.7.13.eb Normal file
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@ -0,0 +1,37 @@
easyblock = 'ConfigureMake'
name = 'CASMcode'
version = "0.2.1"
homepage = 'CASMcode'
description = """CASM (https://github.com/prisms-center/CASMcode) is an open source software
package designed to perform first-principles statistical mechanical studies of multi-component
crystalline solids. CASM interfaces with first-principles electronic structure codes, automates
the construction and parameterization of effective Hamiltonians and subsequently builds highly
optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic
properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry
in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of
freedom in crystalline solids. This includes cluster expansions for configurational disorder
in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational
degrees of freedom involved in structural phase transitions."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = [
'https://github.com/prisms-center/CASMcode/releases/download/v%(version)s/']
sources = ['casm-v%(version)s.tar.gz']
dependencies = [
('Boost', '1.61.0'),
('Python', '2.7.13', '', True),
('SCons', '2.5.1', '-Python-2.7.13', True)
]
configopts = '--with-boost=$EBROOTBOOST'
sanity_check_paths = {
'files': [],
'dirs': ['bin'],
}
moduleclass = 'phys'

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easyblock = 'ConfigureMake'
name = 'CFITSIO'
version = '3.37'
homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
FITS (Flexible Image Transport System) data format."""
toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'optarch': True, 'pic': True}
srcversion = '%s0' % version.replace('.', '')
source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/']
sources = ['%%(namelower)s%s.tar.gz' % srcversion]
sanity_check_paths = {
'files': ["lib/libcfitsio.a"],
'dirs': ["include"],
}
moduleclass = 'lib'

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easyblock = 'ConfigureMake'
name = 'CFITSIO'
version = '3.38'
homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
FITS (Flexible Image Transport System) data format."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True}
srcversion = '%s0' % version.replace('.', '')
source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/']
sources = ['%%(namelower)s%s.tar.gz' % srcversion]
sanity_check_paths = {
'files': ["lib/libcfitsio.a"],
'dirs': ["include"],
}
moduleclass = 'lib'

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@ -0,0 +1,22 @@
easyblock = 'ConfigureMake'
name = 'CFITSIO'
version = '3.38'
homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
FITS (Flexible Image Transport System) data format."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True}
srcversion = '%s0' % version.replace('.', '')
source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/']
sources = ['%%(namelower)s%s.tar.gz' % srcversion]
sanity_check_paths = {
'files': ["lib/libcfitsio.a"],
'dirs': ["include"],
}
moduleclass = 'lib'

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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': 'intel', 'version': '2015b'}
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'

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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]
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'

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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]
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'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.2.3'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': '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', '1.0.1k'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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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': 'foss', 'version': '2015g'}
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'

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@ -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': 'foss', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('ncurses', '6.0')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -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'

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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'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.0'
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': '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'

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@ -0,0 +1,28 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': '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'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': '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', '1.0.1p'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1p'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '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'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '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'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1p'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.3'
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': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1p'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.3'
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': '2016b'}
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'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.4.3'
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': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1p'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.5.1'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.5.2'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.5.2'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'foss', 'version': '2016b'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.5.2'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '2016a'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.5.2'
homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""
toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

31
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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.6.1'
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': 'foss', 'version': '2016b'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

33
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@ -0,0 +1,33 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.6.1'
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': '2016b'}
source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
patches = ['%(name)s-%(version)s-use-gnu11.patch']
configopts = '-- -DCMAKE_USE_OPENSSL=1'
dependencies = [
('ncurses', '6.0'),
# OS dependency should be preferred if the os version is more recent then this version,
# it's nice to have an up to date openssl for security reasons
#('OpenSSL', '1.0.1s'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

31
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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.6.2'
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': '2016b'}
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', '1.0.2j'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

31
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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.6.2'
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': '2016b'}
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', '1.0.2j'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

31
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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.7.1'
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': 'foss', 'version': '2016b'}
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', '1.0.2j'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'CMake'
version = '3.7.1'
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': '2016b'}
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', '1.0.2j'),
]
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
'dirs': [],
}
moduleclass = 'devel'

16
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@ -0,0 +1,16 @@
easyblock = 'Toolchain'
name = 'CORALbenchmark'
version = '1.00'
homepage = 'https://asc.llnl.gov/CORAL-benchmarks'
description = 'Benchmark Codes'
toolchain = {'name': 'foss', 'version': '2016a'}
dependencies = [
('QBOX', 'r140b'),
('LSMS', '3_rev237'),
]
moduleclass = 'tools'

57
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easyblock = 'CMakeMake'
name = 'Caffe'
version = '1.0'
cudaversion = '8.0.44'
versionsuffix = '-CUDA-%s-Python-%%(pyver)s' % cudaversion
homepage = 'https://github.com/BVLC/caffe'
description = """
Caffe is a deep learning framework made with expression, speed,
and modularity in mind. It is developed by the Berkeley Vision
and Learning Center (BVLC) and community contributors.
"""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True}
sources = ['%(version)s.tar.gz']
source_urls = ['https://github.com/BVLC/caffe/archive/']
builddependencies = [
('CMake', '3.8.1', '', True),
]
protobuf_ver = '3.2.0'
dependencies = [
('glog', '0.3.4', '', True),
('gflags', '2.1.2', '', True),
('OpenCV', '3.1.0', '', True),
('CUDA', cudaversion, '', True),
('cuDNN', '5.1', '-CUDA-%s' % cudaversion, True),
('LMDB', '0.9.18', '', True),
('LevelDB', '1.18', '', True),
('snappy', '1.1.3', '', True),
('protobuf', protobuf_ver),
# ('protobuf-python', protobuf_ver, '-Python-%(pyver)s'),
('HDF5', '1.8.16', '-serial'),
('Boost', '1.63.0', '-Python-%(pyver)s'),
('Python', '2.7.13', '', True),
('scikit-image', '0.12.3', '-Python-%(pyver)s', True)
]
configopts = '-DBLAS=open'
modextrapaths = {'PYTHONPATH': ['python']}
sanity_check_paths = {
'files': ['bin/caffe'] +
['include/caffe/proto/caffe.pb.h'],
'dirs': [],
}
sanity_check_commands = [('python', "-c 'import caffe'")]
moduleclass = 'devel'

44
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easyblock = 'SCons'
name = 'Cantera'
version = '2.2.1'
versionsuffix = '-Python-%(pyver)s'
homepage = 'https://github.com/Cantera/cantera'
description = """Chemical kinetics, thermodynamics, and transport tool suite"""
toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = ['https://github.com/Cantera/cantera/archive/']
sources = ['v%(version)s.tar.gz']
dependencies = [
('Python', '2.7.12'),
('Boost', '1.61.0', versionsuffix),
('SUNDIALS', '2.6.2'),
]
builddependencies = [
('SCons', '2.5.0', versionsuffix),
('3to2', '1.1.1', versionsuffix),
]
common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR'
common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
buildopts = 'build ' + common_opts
runtest = 'test ' + common_opts
buildopts = 'install ' + common_opts
prefix_arg = 'prefix='
modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
sanity_check_paths = {
'files': ['bin/mixmaster'],
'dirs': [
'include/cantera',
'lib/pkgconfig',
'lib/python%(pyshortver)s/site-packages'],
}
sanity_check_commands = [('python', "-c 'import cantera'")]
moduleclass = 'chem'

41
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@ -0,0 +1,41 @@
easyblock = 'MakeCp'
name = 'Commet'
version = '20150415'
commit = '4ef0705'
versionsuffix = '-Python-%(pyver)s'
homepage = 'https://colibread.inria.fr/software/commet/'
description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of
a large metagenomic project.
"""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['https://github.com/pierrepeterlongo/commet/archive']
sources = ['%s.tar.gz' % commit]
checksums = ['19cba09ca7a92eaed75ed6af820d9451']
dependencies = [
('Python', '2.7.11'),
]
files_to_copy = ["bin", "doc", "include",
"ABCDE_bench", (["Commet.py"], 'bin')]
sanity_check_paths = {
'files': [
'bin/%s' %
binfile for binfile in [
'Commet.py',
'bvop',
'compare_reads',
'extract_reads',
'filter_reads',
'index_and_search']],
'dirs': [
'doc',
'include']}
moduleclass = 'bio'

34
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@ -0,0 +1,34 @@
easyblock = 'CMakeMake'
name = 'CrossTalkZ'
version = '1.4'
homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/'
description = """
CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment
between pairs of gene or protein groups in large biological networks.
"""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'usempi': True, 'pic': True}
source_urls = [
'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/'
]
sources = ['%(name)s_%(version)s.tgz']
dependencies = [('Boost', '1.60.0')]
builddependencies = [('CMake', '3.4.3',)]
start_dir = 'src'
configopts = " -DBoost_NO_BOOST_CMAKE=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=$EBROOTBOOST"
sanity_check_paths = {
'files': ['bin/CrossTalkZ'],
'dirs': [''],
}
moduleclass = 'bio'

29
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@ -0,0 +1,29 @@
easyblock = 'PythonPackage'
name = 'Cython'
version = '0.24.1'
versionsuffix = '-Python-%(pyver)s'
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."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ]
dependencies = [('Python', '2.7.11')]
cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg'
sanity_check_paths = {
'files': [
'bin/cygdb',
'bin/cython',
'%s/%%(namelower)s.py' %
cythonlibdir],
'dirs': [
cythonlibdir +
'/%(name)s']}
moduleclass = 'lang'

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