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Lukas Krupcik 2017-03-09 11:57:40 +01:00
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name = 'ABAQUS'
version = '6.12.1'
versionsuffix = '-linux-x86_64'
homepage = 'http://www.simulia.com/products/abaqus_fea.html'
description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
toolchain = {'name': 'dummy', 'version': ''}
sources = [SOURCE_TGZ]
builddependencies = [('Java', '1.7.0_60')]
preinstallopts = "export CHECK_DISK_SPACE=OFF && "
moduleclass = 'cae'

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name = 'ABAQUS'
version = '6.13.5'
versionsuffix = '-linux-x86_64'
homepage = 'http://www.simulia.com/products/abaqus_fea.html'
description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
toolchain = {'name': 'dummy', 'version': ''}
sources = [SOURCE_TGZ]
builddependencies = [('Java', '1.7.0_60')]
preinstallopts = "export CHECK_DISK_SPACE=OFF && "
moduleclass = 'cae'

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name = 'ABAQUS'
version = '6.14.1'
versionsuffix = '-linux-x86_64'
homepage = 'http://www.simulia.com/products/abaqus_fea.html'
description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
toolchain = {'name': 'dummy', 'version': ''}
sources = [SOURCE_TGZ]
builddependencies = [('Java', '1.7.0_60')]
preinstallopts = "export CHECK_DISK_SPACE=OFF && "
moduleclass = 'cae'

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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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##
# 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': 'goolf', 'version': '1.5.16'}
# 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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easyblock = 'Tarball'
name = 'ADF'
version = '2014.02'
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': 'dummy', 'version': 'dummy'}
sources = ['%(namelower)s%(version)s.pc64_linux.IntelMPI+CUDA.tgz']
keepsymlinks = True
sanity_check_paths = {
'files': [],
'dirs': ['atomicdata', 'bin', 'examples'],
}
modextravars = {
'ADFHOME': '%(installdir)s',
'ADFBIN': '%(installdir)s/bin',
'ADFRESOURCES': '%(installdir)s/atomicdata',
}
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'

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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'

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easyblock = 'Tarball'
name = 'ADF'
version = '2016.101'
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': 'dummy', 'version': 'dummy'}
sources = ['adf%(version)s.pc64_linux.intelmpi.tgz']
keepsymlinks = True
sanity_check_paths = {
'files': [],
'dirs': ['atomicdata', 'bin', 'examples'],
}
modextravars = {
'ADFHOME': '%(installdir)s',
'ADFBIN': '%(installdir)s/bin',
'ADFRESOURCES': '%(installdir)s/atomicdata',
}
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'

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##
# 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 = 'ConfigureMake'
name = 'ALLPATHS-LG'
version = '46968'
homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/'
description = """ALLPATHS-LG, the new short read genome assembler."""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
# source is moved over time, hence multiple URLs below
source_urls = [
'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code',
'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06',
'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06',
]
sources = ['allpathslg-%(version)s.tar.gz']
sanity_check_paths = {
'files': [],
'dirs': ['bin'],
}
moduleclass = 'bio'

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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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name = 'ANSYS'
version = '18.0'
homepage = 'http://www.ansys.com'
description = """ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater. """
toolchain = {'name': 'dummy', 'version': 'dummy'}
# create a zip file from the 3 install iso files.
# make sure all files of the iso's are in the same directory.
sources = ['ANSYS-18.0.zip']
import os
license_server = os.getenv('EB_ANSYS_LICENSE_SERVER', 'license.it4i.cz')
license_server_port = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
moduleclass = 'tools'

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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Ravi Tripathi
# Email: ravi89@uab.edu
easyblock = "Tarball"
name = 'ASHS'
version = 'rev103_20140612'
homepage = 'https://sites.google.com/site/hipposubfields/home'
description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """
toolchain = {'name': 'dummy', 'version': 'dummy'}
#You need to create an account to download the source
#from https://www.nitrc.org/frs/?group_id=370
sources = ['ashs_Linux64_%(version)s.tgz']
checksums= ["07fea2883b856af8797b200212b72e71"]
modextravars = {'ASHS_ROOT': '%(installdir)s'}
sanity_check_paths = {
'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh",
"bin/ashs_util_makepdf.sh"],
'dirs': ["ext"]
}
moduleclass = 'bio'

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name = 'Advisor'
version = '2016_update2'
homepage = 'https://software.intel.com/intel-advisor-xe'
description = """Vectorization Optimization and Thread Prototyping
- Vectorize & thread code or performance “dies”
- Easy workflow + data + tips = faster code faster
- Prioritize, Prototype & Predict performance gain
"""
toolchain = {'name': 'dummy', 'version': 'dummy'}
sources = ['advisor_xe_%(version)s.tar.gz']
dontcreateinstalldir = 'True'
# license file
import os
license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
moduleclass = 'perf'

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name = 'Advisor'
version = '2017_update1'
homepage = 'https://software.intel.com/intel-advisor-xe'
description = """Vectorization Optimization and Thread Prototyping
- Vectorize & thread code or performance “dies”
- Easy workflow + data + tips = faster code faster
- Prioritize, Prototype & Predict performance gain
"""
toolchain = {'name': 'dummy', 'version': 'dummy'}
sources = ['advisor_%(version)s.tar.gz']
checksums = ['af87b381394be3100507827a3461b3bc']
dontcreateinstalldir = 'True'
# license file
import os
license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
moduleclass = 'perf'

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name = 'Allinea'
version = '4.1-32834-Redhat-5.7-x86_64'
homepage = 'http://www.allinea.com'
description = """The Allinea environment is an essential toolkit for developers and computational scientists
looking to get results faster."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://content.allinea.com/downloads/']
sources = ['%(namelower)s-tools-%(version)s.tar']
# license file
import os
license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic")
moduleclass = 'tools'

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name = 'Allinea'
version = '4.1-32834-Redhat-6.0-x86_64'
homepage = 'http://www.allinea.com'
description = """The Allinea environment is an essential toolkit for developers and computational scientists
looking to get results faster."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://content.allinea.com/downloads/']
sources = ['%(namelower)s-tools-%(version)s.tar']
# license file
import os
license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic")
moduleclass = 'tools'

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name = 'Allinea'
version = '6.1.1-Ubuntu-14.04-x86_64'
homepage = 'http://www.allinea.com'
description = """The Allinea environment is an essential toolkit for developers and computational scientists
looking to get results faster."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://content.allinea.com/downloads/']
sources = ['%(namelower)s-forge-%(version)s.tar']
# Example of templates usage
#templates = [
# 'kebnekaise.qtf',
# 'kebnekaise-gpu.qtf',
#]
# Example of sysconfig usage
#sysconfig = 'system.config.hpc2n'
# license file
license_file = HOME + '/licenses/allinea/license.lic'
moduleclass = 'tools'

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name = 'Amber'
version = '16'
ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1])
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': 'iomkl', 'version': '2016.07'}
toolchainopts = {'usempi': False}
sources = [
'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
patches = ['Amber-%(version)s_fix-hardcoding.patch']
dependencies = [
('netCDF', '4.4.0'),
('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
moduleclass = 'chem'

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name = 'Amber'
version = '16'
ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1])
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': 'iomkl', 'version': '2016.07'}
toolchainopts = {'usempi': True}
sources = [
'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
patches = ['Amber-%(version)s_fix-hardcoding.patch']
dependencies = [
('netCDF', '4.4.0'),
('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
moduleclass = 'chem'

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name = 'Amber'
version = '16'
ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1])
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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'}
toolchainopts = {'usempi': True}
sources = [
'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
patches = ['Amber-%(version)s_fix-hardcoding.patch',
'Amber-%(version)s_test_cuda.patch']
dependencies = [
('CUDA', '7.5.18', '', True),
('netCDF', '4.4.0'),
('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
moduleclass = 'chem'

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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'

22
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@ -0,0 +1,22 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'GCC', 'version': '4.7.2'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.16')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
"autoscan", "autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can adapt the
packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
creates a configuration script for a package from a template file that lists the
operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.18')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
"autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

22
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@ -0,0 +1,22 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.16')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
"autoscan", "autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can adapt the
packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
creates a configuration script for a package from a template file that lists the
operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'intel', 'version': '2017.00'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.17')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
"autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can adapt the
packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
creates a configuration script for a package from a template file that lists the
operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'intel', 'version': '2017a'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.18')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
"autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,26 @@
easyblock = 'ConfigureMake'
name = 'Autoconf'
version = '2.69'
homepage = 'http://www.gnu.org/software/autoconf/'
description = """Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can adapt the
packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
creates a configuration script for a package from a template file that lists the
operating system features that the package can use, in the form of M4 macro calls."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.18')]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
"autoupdate", "ifnames"]],
'dirs': [],
}
moduleclass = 'devel'

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@ -0,0 +1,33 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/
##
easyblock = 'ConfigureMake'
name = 'Automake'
version = "1.15"
homepage = 'http://www.gnu.org/software/automake/automake.html'
description = "Automake: GNU Standards-compliant Makefile generator"
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('Autoconf', '2.69')]
sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
'dirs': []
}
moduleclass = 'devel'

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@ -0,0 +1,33 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/
##
easyblock = 'ConfigureMake'
name = 'Automake'
version = "1.15"
homepage = 'http://www.gnu.org/software/automake/automake.html'
description = "Automake: GNU Standards-compliant Makefile generator"
toolchain = {'name': 'intel', 'version': '2017.00'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('Autoconf', '2.69')]
sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
'dirs': []
}
moduleclass = 'devel'

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@ -0,0 +1,33 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
# Authors:: Fotis Georgatos <fotis@cern.ch>
# License:: MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/
##
easyblock = 'ConfigureMake'
name = 'Automake'
version = "1.15"
homepage = 'http://www.gnu.org/software/automake/automake.html'
description = "Automake: GNU Standards-compliant Makefile generator"
toolchain = {'name': 'intel', 'version': '2017a'}
source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [('Autoconf', '2.69')]
sanity_check_paths = {
'files': ['bin/automake', 'bin/aclocal'],
'dirs': []
}
moduleclass = 'devel'

17
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@ -0,0 +1,17 @@
easyblock = 'Bundle'
name = 'Autotools'
version = '20150215' # date of the most recent change
homepage = 'http://autotools.io'
description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
dependencies = [
('Autoconf', '2.69'), # 20120424
('Automake', '1.15'), # 20150105
('libtool', '2.4.6'), # 20150215
]
moduleclass = 'devel'

17
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@ -0,0 +1,17 @@
easyblock = 'Bundle'
name = 'Autotools'
version = '20150215' # date of the most recent change
homepage = 'http://autotools.io'
description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
toolchain = {'name': 'foss', 'version': '2017a'}
dependencies = [
('Autoconf', '2.69'), # 20120424
('Automake', '1.15'), # 20150105
('libtool', '2.4.6'), # 20150215
]
moduleclass = 'devel'

17
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@ -0,0 +1,17 @@
easyblock = 'Bundle'
name = 'Autotools'
version = '20150215' # date of the most recent change
homepage = 'http://autotools.io'
description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
toolchain = {'name': 'intel', 'version': '2017.00'}
dependencies = [
('Autoconf', '2.69'), # 20120424
('Automake', '1.15'), # 20150105
('libtool', '2.4.6'), # 20150215
]
moduleclass = 'devel'

17
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@ -0,0 +1,17 @@
easyblock = 'Bundle'
name = 'Autotools'
version = '20150215' # date of the most recent change
homepage = 'http://autotools.io'
description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
toolchain = {'name': 'intel', 'version': '2017a'}
dependencies = [
('Autoconf', '2.69'), # 20120424
('Automake', '1.15'), # 20150105
('libtool', '2.4.6'), # 20150215
]
moduleclass = 'devel'

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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'almost'
version = '2.1.0'
homepage = 'http://www-almost.ch.cam.ac.uk/site'
description = """all atom molecular simulation toolkit
- is a fast and flexible molecular modeling environment
that provides powerful and efficient algorithms for molecular
simulation, homology modeling, de novo design and ab-initio
calculations.
"""
toolchain = {'name': 'foss', 'version': '2015b'}
source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ]
builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015b')),
('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '5.1.0-2.25')),
('SQLite', '3.8.8.1', '', ('intel', '2015b')),
('gzip', '1.6', '', ('intel','2015b'))
]
sanity_check_paths = {
'files': ['bin/almost'],
'dirs': []
}
moduleclass = 'bio'

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@ -0,0 +1,44 @@
easyblock = 'ConfigureMake'
name = 'almost'
version = '2.1.0'
homepage = 'http://www-almost.ch.cam.ac.uk/site'
description = """all atom molecular simulation toolkit
- is a fast and flexible molecular modeling environment
that provides powerful and efficient algorithms for molecular
simulation, homology modeling, de novo design and ab-initio
calculations.
"""
toolchain = {'name': 'foss', 'version': '2015g'}
# Sources checked out using svn
# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
# ALMOST 2.1 can be found in branches/almost-2.1
# tar.gz file created from almost-2.1 directory and put to the
# /easybuild/sources
source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ]
builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015g')),
('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '4.9.3-2.25')),
('SQLite', '3.8.8.1'),
('gzip', '1.6'),
('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')),
]
configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
configopts += '--enable-mpi '
preconfigopts = 'autoreconf -fi && automake && '
sanity_check_paths = {
'files': ['bin/almost'],
'dirs': []
}
moduleclass = 'bio'

44
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@ -0,0 +1,44 @@
easyblock = 'ConfigureMake'
name = 'almost'
version = '2.1.0'
homepage = 'http://www-almost.ch.cam.ac.uk/site'
description = """all atom molecular simulation toolkit
- is a fast and flexible molecular modeling environment
that provides powerful and efficient algorithms for molecular
simulation, homology modeling, de novo design and ab-initio
calculations.
"""
toolchain = {'name': 'foss', 'version': '2016a'}
# Sources checked out using svn
# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
# ALMOST 2.1 can be found in branches/almost-2.1
# tar.gz file created from almost-2.1 directory and put to the
# /easybuild/sources
source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ]
builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
('SQLite', '3.8.8.1'),
('gzip', '1.6'),
('Autotools', '20150215'),
]
configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
configopts += '--enable-mpi '
preconfigopts = 'autoreconf -fi && automake && '
sanity_check_paths = {
'files': ['bin/almost'],
'dirs': []
}
moduleclass = 'bio'

31
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@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'
name = 'almost'
version = '2.1.0'
homepage = 'http://www-almost.ch.cam.ac.uk/site'
description = """all atom molecular simulation toolkit
- is a fast and flexible molecular modeling environment
that provides powerful and efficient algorithms for molecular
simulation, homology modeling, de novo design and ab-initio
calculations.
"""
toolchain = {'name': 'intel', 'version': '2015b'}
source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ]
builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015b')),
('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '5.1.0-2.25')),
('SQLite', '3.8.8.1'),
('gzip', '1.6')
]
sanity_check_paths = {
'files': ['bin/almost'],
'dirs': []
}
moduleclass = 'bio'

44
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@ -0,0 +1,44 @@
easyblock = 'ConfigureMake'
name = 'almost'
version = '2.1.0'
homepage = 'http://www-almost.ch.cam.ac.uk/site'
description = """all atom molecular simulation toolkit
- is a fast and flexible molecular modeling environment
that provides powerful and efficient algorithms for molecular
simulation, homology modeling, de novo design and ab-initio
calculations.
"""
toolchain = {'name': 'dummy', 'version': ''}
# Sources checked out using svn
# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
# ALMOST 2.1 can be found in branches/almost-2.1
# tar.gz file created from almost-2.1 directory and put to the
# /easybuild/sources
source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ]
builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
('SQLite', '3.8.8.1'),
('gzip', '1.6'),
('Autotools', '20150215'),
]
configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
configopts += '--enable-mpi '
preconfigopts = 'autoreconf -fi && automake && '
sanity_check_paths = {
'files': ['bin/almost'],
'dirs': []
}
moduleclass = 'bio'

26
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@ -0,0 +1,26 @@
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'

25
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@ -0,0 +1,25 @@
name = 'ant'
version = '1.10.0'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.8.0_112')]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
modextravars = {'ANT_HOME': '%(installdir)s'}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
name = 'ant'
version = '1.8.4'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%s-%s-src.tar.gz' % (name, version)]
source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
java = 'Java'
javaver = '1.7.0_10'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.10', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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View File

@ -0,0 +1,26 @@
name = 'ant'
version = '1.8.4'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%s-%s-src.tar.gz' % (name, version)]
source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
java = 'Java'
javaver = '1.7.0_21'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.10', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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View File

@ -0,0 +1,26 @@
name = 'ant'
version = '1.9.0'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%s-%s-src.tar.gz' % (name, version)]
source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
java = 'Java'
javaver = '1.7.0_15'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': []
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
name = 'ant'
version = '1.9.0'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%s-%s-src.tar.gz' % (name, version)]
source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
java = 'Java'
javaver = '1.7.0_21'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
name = 'ant'
version = '1.9.3'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
java = 'Java'
javaver = '1.7.0_60'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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name = 'ant'
version = '1.9.3'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
java = 'Java'
javaver = '1.7.0_79'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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name = 'ant'
version = '1.9.6'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
java = 'Java'
javaver = '1.7.0_75'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'ant'
version = '1.9.6'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.7.0_79')]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

23
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@ -0,0 +1,23 @@
name = 'ant'
version = '1.9.6'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.7.0_80')]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
name = 'ant'
version = '1.9.6'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
java = 'Java'
javaver = '1.8.0_51'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.11', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

26
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@ -0,0 +1,26 @@
name = 'ant'
version = '1.9.6'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
java = 'Java'
javaver = '1.8.0_66'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
moduleclass = 'devel'

25
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@ -0,0 +1,25 @@
name = 'ant'
version = '1.9.6'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.8.0_72')]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
modextravars = {'ANT_HOME': '%(installdir)s'}
moduleclass = 'devel'

25
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@ -0,0 +1,25 @@
name = 'ant'
version = '1.9.6'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.8.0_77')]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
modextravars = {'ANT_HOME': '%(installdir)s'}
moduleclass = 'devel'

25
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@ -0,0 +1,25 @@
name = 'ant'
version = '1.9.7'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
toolchain = {'name': 'dummy', 'version': ''}
sources = ['apache-%(name)s-%(version)s-src.tar.gz']
source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
dependencies = [('Java', '1.8.0_92')]
builddependencies = [('JUnit', '4.12', versionsuffix)]
sanity_check_paths = {
'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
'dirs': [],
}
modextravars = {'ANT_HOME': '%(installdir)s'}
moduleclass = 'devel'

29
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easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.3'
versionsuffix = '-mt'
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': 'ictce', 'version': '5.3.0'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = [SOURCELOWER_TAR_GZ]
# do not change the order of the patches or things will break
patches = [
'arpack-ng-3.1.3-update-to-head.patch',
'arpack-ng-3.1.3-pkgconfig.patch',
]
configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

29
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easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.3'
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': 'ictce', 'version': '5.3.0'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = [SOURCELOWER_TAR_GZ]
# do not change the order of the patches or things will break
patches = [
'arpack-ng-3.1.3-update-to-head.patch',
'arpack-ng-3.1.3-pkgconfig.patch',
'arpack-ng-3.1.3-configure-mpi.patch',
]
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

29
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@ -0,0 +1,29 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.3'
versionsuffix = '-mt'
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': 'ictce', 'version': '5.5.0'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = [SOURCELOWER_TAR_GZ]
# do not change the order of the patches or things will break
patches = [
'arpack-ng-3.1.3-update-to-head.patch',
'arpack-ng-3.1.3-pkgconfig.patch',
]
configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

29
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@ -0,0 +1,29 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.3'
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': 'ictce', 'version': '5.5.0'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = [SOURCELOWER_TAR_GZ]
# do not change the order of the patches or things will break
patches = [
'arpack-ng-3.1.3-update-to-head.patch',
'arpack-ng-3.1.3-pkgconfig.patch',
'arpack-ng-3.1.3-configure-mpi.patch',
]
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

23
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@ -0,0 +1,23 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.5'
versionsuffix = '-mt'
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': 'ictce', 'version': '7.1.2'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = ['%(name)s_%(version)s.tar.gz']
configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

22
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@ -0,0 +1,22 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.1.5'
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': 'ictce', 'version': '7.1.2'}
toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
sources = ['%(name)s_%(version)s.tar.gz']
configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
'dirs': []
}
moduleclass = 'numlib'

25
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@ -0,0 +1,25 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'GCC', 'version': '4.9.3'}
#toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.3-2.25'))]
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'

25
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@ -0,0 +1,25 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('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'

26
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@ -0,0 +1,26 @@
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'

25
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@ -0,0 +1,25 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'intel', 'version': '2017.00'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('intel', '2017.00'))]
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'

25
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@ -0,0 +1,25 @@
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.4.0'
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': '2017.00'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('intel', '2017.00'))]
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'

36
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@ -0,0 +1,36 @@
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'

36
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@ -0,0 +1,36 @@
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'

34
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@ -0,0 +1,34 @@
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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@ -0,0 +1,39 @@
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'

41
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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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@ -0,0 +1,41 @@
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'

37
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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 = 'BCFtools'
version = '1.3.1'
homepage = 'http://www.htslib.org/'
description = """BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF"""
toolchain = {'name': 'goolf', 'version': '1.7.20'}
source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/']
sources = [SOURCELOWER_TAR_BZ2]
dependencies = [
('zlib', '1.2.8'),
('GSL', '1.16'),
]
buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'"
runtest = 'test'
files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"),
"doc", "plugins", "test", "LICENSE", "README", "AUTHORS"]
sanity_check_paths = {
'files': ["bin/bcftools"],
'dirs': [],
}
moduleclass = 'bio'

36
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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
easyblock = 'MakeCp'
name = "BEDOPS"
version = "2.4.1"
homepage = 'https://github.com/bedops/bedops'
description = """ BEDOPS is an open-source command-line toolkit that performs highly
efficient and scalable Boolean and other set operations, statistical calculations,
archiving, conversion and other management of genomic data of arbitrary scale."""
# this application requires GCC-4.8.x or higher
# be aware if you switch to a different toolchain
toolchain = {'name': 'GCC', 'version': '4.8.4'}
source_urls = ['https://github.com/bedops/bedops/archive/']
sources = ['v%(version)s.tar.gz']
buildopts = ' static && make install'
parallel = 1
files_to_copy = ["bin"]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed",
"starchcat", "vcf2bed", "wig2bed",
"gtf2bed", "bedops", "wig2bed"]],
'dirs': []
}
moduleclass = 'bio'

27
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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
easyblock = "Tarball"
name = 'BLAST'
version = '2.2.26'
versionsuffix = "-Linux_x86_64"
homepage = 'http://blast.ncbi.nlm.nih.gov/'
description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/']
sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz']
sanity_check_paths = {
'files': ["bin/blastall", "bin/impala", "bin/blastpgp"],
'dirs': []
}
moduleclass = 'bio'

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##
# 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>
# License:: MIT/GPL
#
##
name = 'BLAT'
version = '3.5'
homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
source_urls = ['http://users.soe.ucsc.edu/~kent/src']
dependencies = [('libpng', '1.6.2')]
buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
'dirs': files_to_copy,
}
moduleclass = 'bio'

37
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@ -0,0 +1,37 @@
##
# 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>
# License:: MIT/GPL
#
##
name = 'BLAT'
version = '3.5'
homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
toolchain = {'name': 'ictce', 'version': '5.5.0'}
sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
source_urls = ['http://users.soe.ucsc.edu/~kent/src']
libpng = 'libpng'
libpng_ver = '1.6.9'
versionsuffix = '-%s-%s' % (libpng, libpng_ver)
dependencies = [(libpng, libpng_ver)]
buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
'dirs': files_to_copy,
}
moduleclass = 'bio'

33
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@ -0,0 +1,33 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2013 The Cyprus Institute
# Authors:: Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>
# License:: MIT/GPL
#
##
name = 'BLAT'
version = '3.5'
homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
toolchain = {'name': 'ictce', 'version': '5.5.0'}
sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
source_urls = ['http://users.soe.ucsc.edu/~kent/src']
dependencies = [('libpng', '1.6.6')]
buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
'dirs': files_to_copy,
}
moduleclass = 'bio'

23
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@ -0,0 +1,23 @@
easyblock = 'ConfigureMake'
name = 'BLCR'
version = '0.8.5'
homepage = 'http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/'
description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers
are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide
a robust, production quality implementation that checkpoints a wide range of applications,
without requiring changes to be made to application code. """
toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')]
sanity_check_paths = {
'files': ['include/libcr.h'],
'dirs': [],
}
moduleclass = 'lib'

28
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@ -0,0 +1,28 @@
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>, Daniel Navarro <daniel_navarro@meei.harvard.edu>
# License:: MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
##
name = 'BWA'
version = '0.7.13'
homepage = 'http://bio-bwa.sourceforge.net/'
description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference sequence such as the human genome."""
toolchain = {'name': 'goolf', 'version': '1.4.10'}
toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2]
source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
dependencies = [('zlib', '1.2.8')]
moduleclass = 'bio'

28
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@ -0,0 +1,28 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Ravi Tripathi
# Email: ravi89@uab.edu
easyblock = "Tarball"
name = 'BXH_XCEDE_TOOLS'
version = '1.11.1'
homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/'
description = """A collection of data processing and image analysis
tools for data in BXH or XCEDE format. This includes data format
encapsulation/conversion, event-related analysis, QA tools, and more.
These tools form the basis of the fBIRN QA procedures and are also
distributed as part of the fBIRN Data Upload Scripts."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://www.nitrc.org/frs/download.php/7384/']
sources = ['bxh_xcede_tools-%(version)s-lsb30.x86_64.tgz']
sanity_check_paths = {
'files': ["bin/dicom2bxh", "bin/dicom2xcede"],
'dirs': []
}
moduleclass = 'bio'

31
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@ -0,0 +1,31 @@
# 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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@ -0,0 +1,59 @@
# Built with EasyBuild version 2.1.1 on 2015-06-30_09-17-37
##
# 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'
# Build statistics
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40
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@ -0,0 +1,40 @@
# 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 = 'BayPass'
version = '2.1'
homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html'
description = """BayPass is a population genomics software which is primarily aimed at identifying
genetic markers subjected to selection and/or associated to population-specific covariates
(e.g., environmental variables, quantitative or categorical phenotypic characteristics).
The underlying models explicitly account for (and may estimate) the covariance structure among the
population allele frequencies that originates from the shared history of the populations under study"""
toolchain = {'name': 'goolf', 'version': '1.7.20'}
toolchainopts = {'openmp': True}
source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/baypass/files/']
sources = ['%(namelower)s_%(version)s.tar.gz']
start_dir = 'sources'
parallel = 1
files_to_copy = [(['sources/g_baypass'], 'bin/'),
'BayPass_manual_2.1.pdf',
'examples',
'Licence_CeCILL-B_V1-en.txt',
'utils'
]
sanity_check_paths = {
'files': ['bin/g_baypass'],
'dirs': []
}
moduleclass = 'bio'

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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'

31
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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': 'goolf', 'version': '1.4.10'}
toolchainopts = {'openmp': True}
source_urls = ['https://github.com/devillemereuil/bayescenv/archive/']
sources = ['v%(version)s.tar.gz']
start_dir = 'source'
files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog']
parallel = 1
sanity_check_paths = {
'files': ['bin/bayescenv'],
'dirs': [],
}
moduleclass = 'bio'

39
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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 = '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'

40
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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 = 'BayeScan'
version = '2.1'
homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
using differences in allele frequencies between populations."""
# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile
toolchain = {'name': 'goolf', 'version': '1.4.10'}
toolchainopts = {'openmp': True}
source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/']
sources = ['%(name)s%(version)s.zip']
start_dir = 'source'
# fix the makefile which hardcodes g++ compiler
prebuildopts = "sed -i -e 's/g++/${CXX} ${CFLAGS}/g' Makefile && "
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'

27
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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'

30
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# @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp"
name = 'Bazel'
version = '0.3.0'
homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software."""
toolchain = {'name': 'CrayGNU', 'version': '2016.03'}
dependencies = [
('java/jdk1.8.0_51', EXTERNAL_MODULE),
]
sources = ['%(version)s.tar.gz']
source_urls = ['https://github.com/bazelbuild/bazel/archive/']
cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={
'files': ['bin/bazel'],
'dirs': ['bin'],
}
moduleclass = 'devel'

31
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# @author: Robert Schmidt (OHRI)
# @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp"
name = 'Bazel'
version = '0.4.4'
homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software."""
toolchain = {'name': 'dummy', 'version': 'dummy'}
sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s']
dependencies = [
('Java', '1.8.0_121'),
]
cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={
'files': ['bin/bazel'],
'dirs': [],
}
moduleclass = 'devel'

33
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# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
easyblock = "Tarball"
name = 'Beast'
version = '1.8.4'
homepage = 'http://beast.bio.ed.ac.uk/'
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
but is also a framework for testing evolutionary hypotheses without conditioning on a single
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
proportional to its posterior probability. """
toolchain = {'name': 'dummy', 'version': ''}
source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/']
sources = ['BEASTv%(version)s.tgz']
dependencies = [
('Java', '1.8.0_74', '', True),
]
sanity_check_paths = {
'files': ["bin/beast"],
'dirs': []
}
moduleclass = 'bio'

37
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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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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'

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