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# ABINIT recipe
# 2015 Martin Stachon <martin.stachon@vsb.cz>
##
easyblock = "ConfigureMake"
name = 'ABINIT'
version = '7.10.1'
homepage = 'http://www.abinit.org/'
description = """Abinit is a plane wave pseudopotential code for doing
condensed phase electronic structure calculations using DFT."""
toolchain = {'name': 'foss', 'version': '2015b'}
# eg. http://ftp.abinit.org/abinit-7.10.1.tar.gz
sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
source_urls = ['http://ftp.abinit.org/']
# sanity_check_paths = {
# 'files': ["bin/abinit"],
# 'dirs': []
# }
moduleclass = 'chem'
configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
''' --enable-debug="no" ''' + \
''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
name = 'ADF'
version = '2014.11.r48287'
homepage = 'http://www.scm.com/ADF/'
description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
predict chemical structure and reactivity with density functional theory (DFT)."""
toolchain = {'name': 'intel', 'version': '2016a'}
sources = [
'%(namelower)s%(version)s.src.tgz',
# no exact match on revision ID available, but not strictly needed
'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz',
]
license_file = HOME + "/licenses/ADF/license.txt"
modloadmsg = "These environment variables need to be defined before using ADF:\n"
modloadmsg += " * $SCMLICENSE: path to ADF license file\n"
modloadmsg += " * $SCM_TMPDIR: path to user scratch directory"
moduleclass = 'chem'
easyblock = 'CMakeMake'
name = 'ALPS'
version = '2.3.0'
versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
C++ libraries for simplifying the development of such code.
"""
toolchain = {'name': 'foss', 'version': '2016b'}
toolchainopts = {'cstd': 'c++03'}
sources = ['%(namelower)s-%(version)s-src.tar.gz']
source_urls = ['http://alps.comp-phys.org/static/software/releases/']
dependencies = [
('CMake', '3.6.2'),
('Python', '2.7.12'),
('Boost', '1.63.0', versionsuffix),
('HDF5', '1.8.17')
]
separate_build_dir = True
modextravars = {
'ALPS_ROOT': '$root',
}
modextrapaths = {
'PYTHONPATH': ['lib/']
}
sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'],
}
moduleclass = 'phys'
easyblock = 'CMakeMake'
name = 'ALPS'
version = '2.3.0'
versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
C++ libraries for simplifying the development of such code.
"""
toolchain = {'name': 'foss', 'version': '2016b'}
toolchainopts = {'cstd': 'c++03'}
sources = ['%(namelower)s-%(version)s-src.tar.gz']
source_urls = ['http://alps.comp-phys.org/static/software/releases/']
dependencies = [
('CMake', '3.6.2'),
('Python', '3.5.2'),
('Boost', '1.63.0', versionsuffix),
('HDF5', '1.8.17')
]
separate_build_dir = True
modextravars = {
'ALPS_ROOT': '$root',
}
modextrapaths = {
'PYTHONPATH': ['lib/']
}
sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'],
}
moduleclass = 'phys'
#
# modified by Stephane Thiell (Stanford University) for Amber v14
#
# author: Benjamin P. Roberts (University of Auckland)
#
# based on work by Marios Constantinou (University of Cyprus)
#
easyblock = 'ConfigureMake'
name = 'AmberTools'
version = '14'
homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy
Refinement) is software for performing molecular dynamics and structure
prediction."""
toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '15'
sources = [
# 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
configopts = '--no-updates'
# patches = [
# 'Amber-%(version)s_fix-hardcoding.patch',
# 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
#]
dependencies = [
# ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
patchlevels = (13, 13)
patchruns = 1
versionsuffix = '-Python-2.7.11)'
moduleclass = 'chem'
easyblock = 'ConfigureMake'
name = 'AmberTools'
version = '16'
homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy
Refinement) is software for performing molecular dynamics and structure
prediction."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '16'
sources = [
# 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver,
]
patches = [
# 'Amber-%(version)s_fix-hardcoding.patch',
'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
]
dependencies = [
# ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'),
]
patchlevels = (13, 13)
patchruns = 1
versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (
ambertools_ver, patchlevels[0], patchlevels[1])
moduleclass = 'chem'
name = 'Armadillo'
version = '7.500.0'
versionsuffix = '-Python-3.5.2'
homepage = 'http://arma.sourceforge.net/'
description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
as well as a subset of trigonometric and statistics functions."""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = [SOURCELOWER_TAR_XZ]
source_urls = ['http://sourceforge.net/projects/arma/files']
dependencies = [
('Boost', '1.61.0', '-serial'),
('arpack-ng', '3.3.0'),
('CMake', '3.5.2'),
('HDF5', '1.8.16'),
('libxml2', '2.9.3'),
('XZ', '5.2.2'),
]
moduleclass = 'numlib'
easyblock = 'MakeCp'
name = 'angsd'
version = '0.910'
homepage = 'http://www.popgen.dk/angsd'
description = """Program for analysing NGS data."""
toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['https://github.com/ANGSD/angsd/archive/']
sources = ['%(version)s.tar.gz']
dependencies = [('HTSlib', '1.3.1')]
files_to_copy = [
(['angsd'], 'bin'),
'doc',
]
sanity_check_paths = {
'files': ['bin/angsd'],
'dirs': ['doc'],
}
moduleclass = 'bio'
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
builddependencies = [('Autotools', '20150215', '', ('foss', '2016a'))]
preconfigopts = "sh bootstrap && "
configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.so"],
'dirs': []
}
moduleclass = 'numlib'
easyblock = 'ConfigureMake'
name = 'arpack-ng'
version = '3.3.0'
homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
toolchain = {'name': 'intel', 'version': '2015b'}
toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
sources = ['%(version)s.tar.gz']
# IT4I modification: because we have GCC 5.1.0 in intel/2015b toolchain...
builddependencies = [('Autotools', '20150215', '', ('GNU', '5.1.0-2.25'))]
preconfigopts = "sh bootstrap && "
configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.so"],
'dirs': []
}
moduleclass = 'numlib'
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'
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 = {