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This commit is contained in:
Lukáš Krupčík
parent
d8fed5aa5d
commit
57b36493d0
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# ABINIT recipe
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# 2015 Martin Stachon <martin.stachon@vsb.cz>
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##
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easyblock = "ConfigureMake"
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name = 'ABINIT'
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version = '7.10.1'
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homepage = 'http://www.abinit.org/'
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description = """Abinit is a plane wave pseudopotential code for doing
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condensed phase electronic structure calculations using DFT."""
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toolchain = {'name': 'foss', 'version': '2015b'}
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# eg. http://ftp.abinit.org/abinit-7.10.1.tar.gz
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sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
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source_urls = ['http://ftp.abinit.org/']
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# sanity_check_paths = {
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# 'files': ["bin/abinit"],
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# 'dirs': []
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# }
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moduleclass = 'chem'
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configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
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''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
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''' --enable-debug="no" ''' + \
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''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
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@ -1,22 +0,0 @@
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name = 'ADF'
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version = '2014.11.r48287'
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homepage = 'http://www.scm.com/ADF/'
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description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
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predict chemical structure and reactivity with density functional theory (DFT)."""
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toolchain = {'name': 'intel', 'version': '2016a'}
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sources = [
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'%(namelower)s%(version)s.src.tgz',
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# no exact match on revision ID available, but not strictly needed
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'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz',
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]
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license_file = HOME + "/licenses/ADF/license.txt"
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modloadmsg = "These environment variables need to be defined before using ADF:\n"
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modloadmsg += " * $SCMLICENSE: path to ADF license file\n"
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modloadmsg += " * $SCM_TMPDIR: path to user scratch directory"
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moduleclass = 'chem'
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@ -1,40 +0,0 @@
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easyblock = 'CMakeMake'
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name = 'ALPS'
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version = '2.3.0'
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versionsuffix = '-Python-%(pyver)s'
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homepage = "http://alps.comp-phys.org/"
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description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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C++ libraries for simplifying the development of such code.
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"""
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toolchain = {'name': 'foss', 'version': '2016b'}
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toolchainopts = {'cstd': 'c++03'}
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sources = ['%(namelower)s-%(version)s-src.tar.gz']
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source_urls = ['http://alps.comp-phys.org/static/software/releases/']
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dependencies = [
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('CMake', '3.6.2'),
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('Python', '2.7.12'),
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('Boost', '1.63.0', versionsuffix),
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('HDF5', '1.8.17')
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]
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separate_build_dir = True
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modextravars = {
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'ALPS_ROOT': '$root',
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}
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modextrapaths = {
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'PYTHONPATH': ['lib/']
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}
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sanity_check_paths = {
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'files': ['lib/libalps.%s' % SHLIB_EXT],
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'dirs': ['include/alps', 'bin/', 'share/'],
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}
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moduleclass = 'phys'
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@ -1,40 +0,0 @@
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easyblock = 'CMakeMake'
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name = 'ALPS'
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version = '2.3.0'
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versionsuffix = '-Python-%(pyver)s'
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homepage = "http://alps.comp-phys.org/"
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description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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C++ libraries for simplifying the development of such code.
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"""
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toolchain = {'name': 'foss', 'version': '2016b'}
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toolchainopts = {'cstd': 'c++03'}
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sources = ['%(namelower)s-%(version)s-src.tar.gz']
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source_urls = ['http://alps.comp-phys.org/static/software/releases/']
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dependencies = [
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('CMake', '3.6.2'),
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('Python', '3.5.2'),
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('Boost', '1.63.0', versionsuffix),
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('HDF5', '1.8.17')
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]
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separate_build_dir = True
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modextravars = {
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'ALPS_ROOT': '$root',
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}
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modextrapaths = {
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'PYTHONPATH': ['lib/']
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}
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sanity_check_paths = {
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'files': ['lib/libalps.%s' % SHLIB_EXT],
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'dirs': ['include/alps', 'bin/', 'share/'],
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}
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moduleclass = 'phys'
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@ -1,46 +0,0 @@
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#
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# modified by Stephane Thiell (Stanford University) for Amber v14
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#
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# author: Benjamin P. Roberts (University of Auckland)
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#
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# based on work by Marios Constantinou (University of Cyprus)
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#
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easyblock = 'ConfigureMake'
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name = 'AmberTools'
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version = '14'
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homepage = 'http://ambermd.org/amber.html'
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description = """Amber (originally Assisted Model Building with Energy
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Refinement) is software for performing molecular dynamics and structure
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prediction."""
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toolchain = {'name': 'intel', 'version': '2016a'}
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toolchainopts = {'openmp': False, 'usempi': True}
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ambertools_ver = '15'
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sources = [
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# 'Amber%(version)s.tar.bz2',
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'AmberTools%s.tar.bz2' % ambertools_ver,
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]
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configopts = '--no-updates'
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# patches = [
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# 'Amber-%(version)s_fix-hardcoding.patch',
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# 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
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#]
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dependencies = [
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# ('CUDA', '7.5.18', '', True),
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# ('netCDF', '4.4.0'),
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# ('netCDF-Fortran', '4.4.4'),
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('Python', '2.7.11'),
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]
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patchlevels = (13, 13)
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patchruns = 1
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versionsuffix = '-Python-2.7.11)'
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moduleclass = 'chem'
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easyblock = 'ConfigureMake'
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name = 'AmberTools'
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version = '16'
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homepage = 'http://ambermd.org/amber.html'
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description = """Amber (originally Assisted Model Building with Energy
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Refinement) is software for performing molecular dynamics and structure
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prediction."""
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toolchain = {'name': 'intel', 'version': '2015b'}
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toolchainopts = {'openmp': False, 'usempi': True}
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ambertools_ver = '16'
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sources = [
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# 'Amber%(version)s.tar.bz2',
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'AmberTools%s.tar.bz2' % ambertools_ver,
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]
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patches = [
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# 'Amber-%(version)s_fix-hardcoding.patch',
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'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
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]
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dependencies = [
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# ('CUDA', '7.5.18', '', True),
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# ('netCDF', '4.4.0'),
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# ('netCDF-Fortran', '4.4.4'),
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('Python', '2.7.11'),
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]
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patchlevels = (13, 13)
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patchruns = 1
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versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (
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ambertools_ver, patchlevels[0], patchlevels[1])
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moduleclass = 'chem'
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@ -1,24 +0,0 @@
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name = 'Armadillo'
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version = '7.500.0'
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versionsuffix = '-Python-3.5.2'
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homepage = 'http://arma.sourceforge.net/'
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description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
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a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
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as well as a subset of trigonometric and statistics functions."""
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toolchain = {'name': 'foss', 'version': '2016a'}
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sources = [SOURCELOWER_TAR_XZ]
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source_urls = ['http://sourceforge.net/projects/arma/files']
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dependencies = [
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('Boost', '1.61.0', '-serial'),
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('arpack-ng', '3.3.0'),
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('CMake', '3.5.2'),
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('HDF5', '1.8.16'),
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('libxml2', '2.9.3'),
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('XZ', '5.2.2'),
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]
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moduleclass = 'numlib'
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easyblock = 'MakeCp'
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name = 'angsd'
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version = '0.910'
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homepage = 'http://www.popgen.dk/angsd'
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description = """Program for analysing NGS data."""
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toolchain = {'name': 'foss', 'version': '2016a'}
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source_urls = ['https://github.com/ANGSD/angsd/archive/']
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sources = ['%(version)s.tar.gz']
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dependencies = [('HTSlib', '1.3.1')]
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files_to_copy = [
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(['angsd'], 'bin'),
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'doc',
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]
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sanity_check_paths = {
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'files': ['bin/angsd'],
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'dirs': ['doc'],
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}
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moduleclass = 'bio'
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easyblock = 'ConfigureMake'
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name = 'arpack-ng'
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version = '3.3.0'
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homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
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description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
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toolchain = {'name': 'foss', 'version': '2016a'}
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toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
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source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
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sources = ['%(version)s.tar.gz']
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builddependencies = [('Autotools', '20150215', '', ('foss', '2016a'))]
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preconfigopts = "sh bootstrap && "
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configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
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sanity_check_paths = {
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'files': ["lib/libarpack.a", "lib/libarpack.so"],
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'dirs': []
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}
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moduleclass = 'numlib'
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easyblock = 'ConfigureMake'
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name = 'arpack-ng'
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version = '3.3.0'
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homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
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description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
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toolchain = {'name': 'intel', 'version': '2015b'}
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toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
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source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
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sources = ['%(version)s.tar.gz']
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# IT4I modification: because we have GCC 5.1.0 in intel/2015b toolchain...
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builddependencies = [('Autotools', '20150215', '', ('GNU', '5.1.0-2.25'))]
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preconfigopts = "sh bootstrap && "
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configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
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sanity_check_paths = {
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'files': ["lib/libarpack.a", "lib/libarpack.so"],
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'dirs': []
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}
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moduleclass = 'numlib'
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@ -1,36 +0,0 @@
|
||||
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'
|
||||
@ -1,36 +0,0 @@
|
||||
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'
|
||||
@ -1,34 +0,0 @@
|
||||
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'
|
||||
@ -1,45 +0,0 @@
|
||||
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'
|
||||
@ -1,45 +0,0 @@
|
||||
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'
|
||||
@ -1,43 +0,0 @@
|
||||
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'
|
||||
@ -1,47 +0,0 @@
|
||||
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="$CFLAGS" USE_GSL=1'
|
||||
installopts = ' prefix=%(installdir)s'
|
||||
|
||||
postinstallcmds = [
|
||||
'mkdir -p %(installdir)s/lib/plugins',
|
||||
'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [
|
||||
'bin/%s' %
|
||||
x for x in [
|
||||
'bcftools',
|
||||
'plot-vcfstats',
|
||||
'vcfutils.pl']],
|
||||
'dirs': ['lib/plugins'],
|
||||
}
|
||||
|
||||
moduleclass = 'bio'
|
||||
@ -1,47 +0,0 @@
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'BCFtools'
|
||||
version = '1.3'
|
||||
|
||||
homepage = 'http://www.htslib.org/'
|
||||
description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
|
||||
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2016a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
|
||||
|
||||
dependencies = [
|
||||
('zlib', '1.2.8'),
|
||||
('HTSlib', '1.3'),
|
||||
('GSL', '2.1'),
|
||||
]
|
||||
|
||||
parallel = 1
|
||||
|
||||
skipsteps = ['configure']
|
||||
|
||||
buildopts = 'CC="$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'
|
||||
@ -1,31 +0,0 @@
|
||||
# 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'
|
||||
@ -1,33 +0,0 @@
|
||||
##
|
||||
# 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'
|
||||
@ -1,33 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = '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'
|
||||
@ -1,39 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = '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'
|
||||
@ -1,28 +0,0 @@
|
||||
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'
|
||||
@ -1,37 +0,0 @@
|
||||
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'
|
||||
@ -1,37 +0,0 @@
|
||||
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'
|
||||
@ -1,39 +0,0 @@
|
||||
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'
|
||||
@ -1,38 +0,0 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
#
|
||||
# Copyright:: Copyright 2012-2013 The Cyprus Institute
|
||||
# Authors:: Andreas Panteli <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'
|
||||
@ -1,42 +0,0 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
#
|
||||
# Copyright:: Copyright 2012-2013 The Cyprus Institute
|
||||
# Authors:: Andreas Panteli <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'
|
||||
@ -1,38 +0,0 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
#
|
||||
# Copyright:: Copyright 2012-2013 The Cyprus Institute
|
||||
# Authors:: Andreas Panteli <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'
|
||||
@ -1,38 +0,0 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
#
|
||||
# Copyright:: Copyright 2012-2013 The Cyprus Institute
|
||||
# Authors:: Andreas Panteli <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'
|
||||
@ -1,26 +0,0 @@
|
||||
# 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'
|
||||
@ -1,25 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,26 +0,0 @@
|
||||
# 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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,21 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,25 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,21 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,23 +0,0 @@
|
||||
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'
|
||||
@ -1,27 +0,0 @@
|
||||
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'
|
||||
@ -1,28 +0,0 @@
|
||||
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'
|
||||
@ -1,55 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,55 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,55 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,57 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,57 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,57 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,57 +0,0 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
# 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'
|
||||
@ -1,32 +0,0 @@
|
||||
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'
|
||||
@ -1,32 +0,0 @@
|
||||
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'
|
||||
@ -1,35 +0,0 @@
|
||||
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'
|
||||
@ -1,36 +0,0 @@
|
||||
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'
|
||||
@ -1,37 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,22 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'CMake'
|
||||
version = '3.3.2'
|
||||
|
||||
homepage = 'http://www.cmake.org'
|
||||
description = """CMake, the cross-platform, open-source build system.
|
||||
CMake is a family of tools designed to build, test and package software."""
|
||||
|
||||
toolchain = {'name': '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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,28 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,33 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,31 +0,0 @@
|
||||
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'
|
||||
@ -1,16 +0,0 @@
|
||||
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'
|
||||
@ -1,57 +0,0 @@
|
||||
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'
|
||||
@ -1,44 +0,0 @@
|
||||
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'
|
||||
@ -1,41 +0,0 @@
|
||||
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'
|
||||
@ -1,34 +0,0 @@
|
||||
easyblock = 'CMakeMake'
|
||||
|
||||
name = 'CrossTalkZ'
|
||||
version = '1.4'
|
||||
|
||||
homepage = 'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/'
|
||||
description = """
|
||||
CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment
|
||||
between pairs of gene or protein groups in large biological networks.
|
||||
"""
|
||||
|
||||
toolchain = {'name': 'foss', 'version': '2016a'}
|
||||
toolchainopts = {'usempi': True, 'pic': True}
|
||||
|
||||
source_urls = [
|
||||
'http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/'
|
||||
]
|
||||
sources = ['%(name)s_%(version)s.tgz']
|
||||
|
||||
dependencies = [('Boost', '1.60.0')]
|
||||
|
||||
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'
|
||||
@ -1,29 +0,0 @@
|
||||
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'
|
||||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue
Block a user