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This commit is contained in:
Lukáš Krupčík 2018-10-03 07:48:02 +02:00
parent e3338cde79
commit 92cb0848fe
1669 changed files with 12954 additions and 6104 deletions
a
ABINIT
ABINIT-7.10.1-foss-2015b.ebABINIT-7.10.1-goolf-1.5.16.ebABINIT-8.2.2-intel-2017a.ebABINIT-8.6.1-intel-2017a.eb
ACTC
ACTC-1.1-intel-2017a.eb
ALAMODE
ALAMODE-0.9.8-intel-2017a.eb
ALPS
ALPS-2.3.0-foss-2016b-Python-2.7.12.ebALPS-2.3.0-foss-2016b-Python-3.5.2.eb
ALPScore
ALPScore-2.1.1-intel-2017b.eb
ANSYS
ANSYS-18.0-intel-2017a.ebANSYS-18.0.ebANSYS-18.2-intel-2017a.ebANSYS-19.0-intel-2017b-X11.eb
APR-util
APR-util-1.5.4.eb
APR
APR-1.5.2.eb
ASE
ASE-3.15.0-Py-3.6.ebASE-3.15.0-Python-2.7.13-base-test.ebASE-3.15.0-Python-2.7.13-base.ebASE-3.15.0-Python-3.6.4-base-test.ebASE-3.15.0-intel-2017a-Python-2.7.13.eb
ASHS
ASHS-rev103_20140612.eb
ATLAS
ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.ebATLAS-3.10.3-GCC-5.4.0-2.26-LAPACK-3.6.1.ebATLAS-3.10.3-GCC-6.3.0-2.27-LAPACK-3.6.1.eb
Amber
Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.ebAmber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.ebAmber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.ebAmber-18-iomkl-2017b-AmberTools-18-serial.eb
AmberTools
AmberTools-15-intel-2015b-Python-2.7.11.ebAmberTools-16-intel-2015b-Python-2.7.11.eb
Autoconf
Autoconf-2.69.eb
almost
almost-2.1.0.eb
angsd
angsd-0.910-foss-2016a.eb
ant
ant-1.10.0-Java-1.8.0_112.ebant-1.9.7-Java-1.8.0_121.ebant-1.9.7-Java-1.8.0_92.eb
arpack-ng
arpack-ng-3.1.3-ictce-5.3.0.ebarpack-ng-3.1.3-ictce-5.5.0.eb
asn1crypto
asn1crypto-0.24.0-Py-2.7.eb
astor
astor-0.6.2-Py-3.6.eb
astroid
astroid-1.5.3-Python-2.7.13-base.eb
asv
asv-0.2.1-Py-2.7.ebasv-0.2.1-Py-3.6.eb
b
BBMap
BBMap-35.82-foss-2015b-Java-1.8.0_66.ebBBMap-35.82-foss-2015b-Java-1.8.0_74.ebBBMap-36.62-intel-2016b-Java-1.8.0_112.eb
BCFtools
BCFtools-1.2-foss-2015a.ebBCFtools-1.2-intel-2015a.ebBCFtools-1.3-foss-2015g.ebBCFtools-1.3-foss-2016a.ebBCFtools-1.3-intel-2016a.ebBCFtools-1.3.1-goolf-1.7.20.ebBCFtools-1.6-intel-2017a.ebBCFtools-1.8-intel-2017a.eb
BEDOPS
BEDOPS-2.4.1-GCC-4.8.4.eb
BLAST
BLAST-2.2.26-Linux_x86_64.eb
BLAT
BLAT-3.5-goolf-1.4.10.ebBLAT-3.5-ictce-5.5.0-libpng-1.6.9.ebBLAT-3.5-ictce-5.5.0.eb
BLCR
BLCR-0.8.5-GNU-5.1.0-2.25.eb
BWA
BWA-0.7.17-intel-2017a.eb
BXH_XCEDE_TOOLS
BXH_XCEDE_TOOLS-1.11.1.eb
Bash
Bash-4.2-intel-2015b.eb
BayPass
BayPass-2.1-goolf-1.7.20.eb
BayeScEnv
BayeScEnv-1.1-foss-2016a.ebBayeScEnv-1.1-goolf-1.4.10.eb
BayeScan
BayeScan-2.1-foss-2016a.ebBayeScan-2.1-goolf-1.4.10.eb
BayesAss
BayesAss-3.0.4-foss-2016a.eb
Bazel
Bazel-0.3.0-CrayGNU-2016.03.ebBazel-0.4.4.ebBazel-0.5.0-GCC-4.9.3-tf.ebBazel-0.5.0-GCC-7.1.0-2.28.ebBazel-0.5.1-GCC-7.1.0-2.28.ebBazel-0.5.4-GCC-7.1.0-2.28.ebBazel-0.7.0-GCC-6.3.0-2.27.ebBazel-0.7.0-GCC-7.1.0-2.28.eb
Beast
Beast-1.8.4.eb
BerkeleyGW
BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.ebBerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb
BerkeleyUPC
BerkeleyUPC-2.16.2-gompi-2015b.eb
BioPerl
BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb
Biopython
Biopython-1.61-goolf-1.4.10-Python-2.7.3.ebBiopython-1.61-ictce-5.3.0-Python-2.7.3.ebBiopython-1.65-foss-2016a-Python-2.7.11.ebBiopython-1.68-foss-2016b-Python-2.7.12.ebBiopython-1.68-intel-2016b-Python-2.7.12.ebBiopython-1.68-intel-2016b-Python-3.5.2.eb
BoltzTraP2
BoltzTraP2-18.1.1-Py-3.6.ebBoltzTraP2-18.1.2-Py-3.6.eb
Boost
Boost-1.49.0-goolf-1.5.16-Python-2.7.3.ebBoost-1.58.0-gompi-2015e-Python-2.7.9.ebBoost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb
Bowtie2
Bowtie2-2.0.5-goolf-1.4.10.ebBowtie2-2.0.6-goolf-1.4.10.ebBowtie2-2.1.0-goolf-1.4.10.ebBowtie2-2.2.0-goolf-1.4.10.ebBowtie2-2.2.2-goolf-1.4.10.ebBowtie2-2.2.4-goolf-1.4.10.ebBowtie2-2.2.5-goolf-1.7.20.eb
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10
a/ABINIT/ABINIT-7.10.1-foss-2015b.eb

@ -17,14 +17,14 @@ toolchain = {'name': 'foss', 'version': '2015b'}
sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')] sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
source_urls = ['http://ftp.abinit.org/'] source_urls = ['http://ftp.abinit.org/']
#sanity_check_paths = { # sanity_check_paths = {
# 'files': ["bin/abinit"], # 'files': ["bin/abinit"],
# 'dirs': [] # 'dirs': []
# } # }
moduleclass = 'chem' moduleclass = 'chem'
configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \ 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-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
''' --enable-debug="no" ''' + \ ''' --enable-debug="no" ''' + \
''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"''' ''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''

11
a/ABINIT/ABINIT-7.10.1-goolf-1.5.16.eb

@ -18,15 +18,14 @@ toolchain = {'name': 'goolf', 'version': '1.5.16'}
sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')] sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
source_urls = ['http://ftp.abinit.org/'] source_urls = ['http://ftp.abinit.org/']
#sanity_check_paths = { # sanity_check_paths = {
# 'files': ["bin/abinit"], # 'files': ["bin/abinit"],
# 'dirs': [] # 'dirs': []
# } # }
moduleclass = 'chem' moduleclass = 'chem'
configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \ 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-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
''' --enable-debug="no" ''' + \ ''' --enable-debug="no" ''' + \
''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"''' ''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''

11
a/ABINIT/ABINIT-8.2.2-intel-2017a.eb

@ -26,7 +26,16 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'files': [
'bin/%s' %
x for x in [
'abinit',
'aim',
'cut3d',
'conducti',
'mrgddb',
'mrgscr',
'optic']],
'dirs': ['lib/pkgconfig'], 'dirs': ['lib/pkgconfig'],
} }

15
a/ABINIT/ABINIT-8.6.1-intel-2017a.eb

@ -21,12 +21,21 @@ configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$
dependencies = [ dependencies = [
('libxc', '4.0.2'), ('libxc', '4.0.2'),
# ('netCDF', '4.4.1.1'), # ('netCDF', '4.4.1.1'),
# ('netCDF-Fortran', '4.4.4'), # ('netCDF-Fortran', '4.4.4'),
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'files': [
'bin/%s' %
x for x in [
'abinit',
'aim',
'cut3d',
'conducti',
'mrgddb',
'mrgscr',
'optic']],
'dirs': ['lib/pkgconfig'], 'dirs': ['lib/pkgconfig'],
} }

12
a/ACTC/ACTC-1.1-intel-2017a.eb

@ -23,8 +23,16 @@ files_to_copy = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', 'files': [
'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], 'bin/tctest',
'bin/tctest2',
'bin/tcsample',
'include/ac/tc.h',
'lib/libactc.a',
'COPYRIGHT',
'manual.html',
'prims.gif',
'README'],
'dirs': [], 'dirs': [],
} }

22
a/ALAMODE/ALAMODE-0.9.8-intel-2017a.eb

@ -4,10 +4,10 @@ name = 'ALAMODE'
version = '0.9.8' version = '0.9.8'
homepage = 'http://alamode.readthedocs.io/' homepage = 'http://alamode.readthedocs.io/'
description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity
and lattice thermal conductivity of solids. By using an external DFT package such as VASP and and lattice thermal conductivity of solids. By using an external DFT package such as VASP and
Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly
with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice
thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.""" thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles."""
toolchain = {'name': 'intel', 'version': '2017a'} toolchain = {'name': 'intel', 'version': '2017a'}
@ -16,10 +16,10 @@ source_urls = [SOURCEFORGE_SOURCE]
sources = [SOURCELOWER_TAR_GZ] sources = [SOURCELOWER_TAR_GZ]
dependencies = [ dependencies = [
('Boost', '1.63.0'), ('Boost', '1.63.0'),
('Python', '2.7.13-base', '', True), ('Python', '2.7.13-base', '', True),
('matplotlib', '2.0.2-Python-2.7.13-base', '', True), ('matplotlib', '2.0.2-Python-2.7.13-base', '', True),
('numpy', '1.13.0-Python-2.7.13-base', '', True), ('numpy', '1.13.0-Python-2.7.13-base', '', True),
] ]
commands = "cd alm && mv Makefile.linux Makefile && make && cd .. && " commands = "cd alm && mv Makefile.linux Makefile && make && cd .. && "
@ -29,9 +29,9 @@ commands += "cd tools && make "
cmds_map = [('.*', commands)] cmds_map = [('.*', commands)]
files_to_copy = [ files_to_copy = [
(['alm/alm', 'anphon/anphon'], 'bin'), (['alm/alm', 'anphon/anphon'], 'bin'),
(['tools/analyze_phonons', 'tools/qe2alm'], 'tools'), (['tools/analyze_phonons', 'tools/qe2alm'], 'tools'),
(['tools/*.py'], 'tools'), (['tools/*.py'], 'tools'),
] ]
modextrapaths = {'PATH': 'tools'} modextrapaths = {'PATH': 'tools'}

4
a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb

@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/" homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort 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 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. C++ libraries for simplifying the development of such code.
""" """
@ -32,7 +32,7 @@ modextrapaths = {
'PYTHONPATH': ['lib/'] 'PYTHONPATH': ['lib/']
} }
sanity_check_paths={ sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT], 'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'], 'dirs': ['include/alps', 'bin/', 'share/'],
} }

4
a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb

@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s'
homepage = "http://alps.comp-phys.org/" homepage = "http://alps.comp-phys.org/"
description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort 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 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. C++ libraries for simplifying the development of such code.
""" """
@ -32,7 +32,7 @@ modextrapaths = {
'PYTHONPATH': ['lib/'] 'PYTHONPATH': ['lib/']
} }
sanity_check_paths={ sanity_check_paths = {
'files': ['lib/libalps.%s' % SHLIB_EXT], 'files': ['lib/libalps.%s' % SHLIB_EXT],
'dirs': ['include/alps', 'bin/', 'share/'], 'dirs': ['include/alps', 'bin/', 'share/'],
} }

15
a/ALPScore/ALPScore-2.1.1-intel-2017b.eb

@ -29,9 +29,18 @@ modextravars = {
'ALPS_ROOT': '$root', 'ALPS_ROOT': '$root',
} }
sanity_check_paths={ sanity_check_paths = {
'files': ['lib/libalps-accumulators.so', 'lib/libalps-gf.so', 'lib/libalps-hdf5.so', 'lib/libalps-mc.so', 'lib/libalps-params.so', 'lib/libalps-utilities.so'], 'files': [
'dirs': ['include/alps', 'lib/', 'share/'], 'lib/libalps-accumulators.so',
'lib/libalps-gf.so',
'lib/libalps-hdf5.so',
'lib/libalps-mc.so',
'lib/libalps-params.so',
'lib/libalps-utilities.so'],
'dirs': [
'include/alps',
'lib/',
'share/'],
} }
moduleclass = 'phys' moduleclass = 'phys'

6
a/ANSYS/ANSYS-18.0-intel-2017a.eb

@ -4,8 +4,8 @@ name = 'ANSYS'
version = '18.0' version = '18.0'
homepage = 'http://www.ansys.com' homepage = 'http://www.ansys.com'
description = """ANSYS simulation software enables organizations to confidently predict description = """ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is how their products will operate in the real world. We believe that every product is
a promise of something greater. """ a promise of something greater. """
toolchain = {'name': 'intel', 'version': '2017a'} toolchain = {'name': 'intel', 'version': '2017a'}
@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
sources = ['ANSYS-18.0.zip'] sources = ['ANSYS-18.0.zip']
dependencies = [ dependencies = [
('libpng', '1.2.59', '', True) ('libpng', '1.2.59', '', True)
] ]
import os import os

6
a/ANSYS/ANSYS-18.0.eb

@ -4,8 +4,8 @@ name = 'ANSYS'
version = '18.0' version = '18.0'
homepage = 'http://www.ansys.com' homepage = 'http://www.ansys.com'
description = """ANSYS simulation software enables organizations to confidently predict description = """ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is how their products will operate in the real world. We believe that every product is
a promise of something greater. """ a promise of something greater. """
toolchain = {'name': 'dummy', 'version': ''} toolchain = {'name': 'dummy', 'version': ''}
@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': ''}
sources = ['ANSYS-18.0.zip'] sources = ['ANSYS-18.0.zip']
dependencies = [ dependencies = [
('libpng', '1.2.59', '', True) ('libpng', '1.2.59', '', True)
] ]
import os import os

4
a/ANSYS/ANSYS-18.2-intel-2017a.eb

@ -15,8 +15,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
sources = ['ANSYS-18.2.zip'] sources = ['ANSYS-18.2.zip']
dependencies = [ dependencies = [
('libpng', '1.2.59', '', True), ('libpng', '1.2.59', '', True),
# ('libX11', '1.6.3', '', True), # ('libX11', '1.6.3', '', True),
] ]
import os import os

8
a/ANSYS/ANSYS-19.0-intel-2017b-X11.eb

@ -16,12 +16,12 @@ toolchain = {'name': 'intel', 'version': '2017b'}
sources = ['ANSYS-19.0.zip'] sources = ['ANSYS-19.0.zip']
dependencies = [ dependencies = [
# ('libpng', '1.2.59', '', True), # ('libpng', '1.2.59', '', True),
# ('libXrender', '0.9.9', '', True), # ('libXrender', '0.9.9', '', True),
('X11', '20170314', '', True), ('X11', '20170314', '', True),
] ]
#modextrapaths = { # modextrapaths = {
# 'LD_LIBRARY_PATH': ['$LD_LIBRARY_PATH:%(installdir)s/v190/Electronics/Linux64/defer:%(installdir)s/v190/Framework/bin/Linux64'], # 'LD_LIBRARY_PATH': ['$LD_LIBRARY_PATH:%(installdir)s/v190/Electronics/Linux64/defer:%(installdir)s/v190/Framework/bin/Linux64'],
# 'LD_LIBRARY_PATH': 'v190/Electronics/Linux64/defer', # 'LD_LIBRARY_PATH': 'v190/Electronics/Linux64/defer',
# 'LD_LIBRARY_PATH': 'v190/Framework/bin/Linux64', # 'LD_LIBRARY_PATH': 'v190/Framework/bin/Linux64',

6
a/APR-util/APR-util-1.5.4.eb

@ -20,7 +20,11 @@ dependencies = [
configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT "
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], 'files': [
"bin/apu-1-config",
"lib/libaprutil-1.%s" %
SHLIB_EXT,
"lib/libaprutil-1.a"],
'dirs': ["include/apr-1"], 'dirs': ["include/apr-1"],
} }

6
a/APR/APR-1.5.2.eb

@ -12,7 +12,11 @@ source_urls = ['http://archive.apache.org/dist/apr/']
sources = [SOURCELOWER_TAR_GZ] sources = [SOURCELOWER_TAR_GZ]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], 'files': [
"bin/apr-1-config",
"lib/libapr-1.%s" %
SHLIB_EXT,
"lib/libapr-1.a"],
'dirs': ["include/apr-1"], 'dirs': ["include/apr-1"],
} }

7
a/ASE/ASE-3.15.0-Py-3.6.eb

@ -23,7 +23,12 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], 'files': [
'bin/ase-build',
'bin/ase-db',
'bin/ase-gui',
'bin/ase-info',
'bin/ase-run'],
'dirs': ['lib/python3.6/site-packages'], 'dirs': ['lib/python3.6/site-packages'],
} }

13
a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb

@ -18,13 +18,18 @@ checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
dependencies = [ dependencies = [
('Python', '2.7.13'), ('Python', '2.7.13'),
# ('numpy', '1.13.0', '-Python-2.7.13-base'), # ('numpy', '1.13.0', '-Python-2.7.13-base'),
# ('scipy', '0.19.1', '-Python-2.7.13-base'), # ('scipy', '0.19.1', '-Python-2.7.13-base'),
# ('matplotlib', '2.0.2', '-Python-2.7.13-base'), # ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], 'files': [
'bin/ase-build',
'bin/ase-db',
'bin/ase-gui',
'bin/ase-info',
'bin/ase-run'],
'dirs': ['lib/python%(pyshortver)s/site-packages'], 'dirs': ['lib/python%(pyshortver)s/site-packages'],
} }

7
a/ASE/ASE-3.15.0-Python-2.7.13-base.eb

@ -24,7 +24,12 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], 'files': [
'bin/ase-build',
'bin/ase-db',
'bin/ase-gui',
'bin/ase-info',
'bin/ase-run'],
'dirs': ['lib/python%(pyshortver)s/site-packages'], 'dirs': ['lib/python%(pyshortver)s/site-packages'],
} }

13
a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb

@ -18,13 +18,18 @@ checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
dependencies = [ dependencies = [
('Python', '3.6.1'), ('Python', '3.6.1'),
# ('numpy', '1.13.0', '-Python-2.7.13-base'), # ('numpy', '1.13.0', '-Python-2.7.13-base'),
# ('scipy', '0.19.1', '-Python-2.7.13-base'), # ('scipy', '0.19.1', '-Python-2.7.13-base'),
# ('matplotlib', '2.0.2', '-Python-2.7.13-base'), # ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], 'files': [
'bin/ase-build',
'bin/ase-db',
'bin/ase-gui',
'bin/ase-info',
'bin/ase-run'],
'dirs': ['lib/python%(pyshortver)s/site-packages'], 'dirs': ['lib/python%(pyshortver)s/site-packages'],
} }

7
a/ASE/ASE-3.15.0-intel-2017a-Python-2.7.13.eb

@ -22,7 +22,12 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], 'files': [
'bin/ase-build',
'bin/ase-db',
'bin/ase-gui',
'bin/ase-info',
'bin/ase-run'],
'dirs': ['lib/python%(pyshortver)s/site-packages'], 'dirs': ['lib/python%(pyshortver)s/site-packages'],
} }

16
a/ASHS/ASHS-rev103_20140612.eb

@ -12,18 +12,20 @@ description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """
toolchain = {'name': 'dummy', 'version': 'dummy'} toolchain = {'name': 'dummy', 'version': 'dummy'}
#You need to create an account to download the source # You need to create an account to download the source
#from https://www.nitrc.org/frs/?group_id=370 # from https://www.nitrc.org/frs/?group_id=370
sources = ['ashs_Linux64_%(version)s.tgz'] sources = ['ashs_Linux64_%(version)s.tgz']
checksums= ["07fea2883b856af8797b200212b72e71"] checksums = ["07fea2883b856af8797b200212b72e71"]
modextravars = {'ASHS_ROOT': '%(installdir)s'} modextravars = {'ASHS_ROOT': '%(installdir)s'}
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", 'files': [
"bin/ashs_util_makepdf.sh"], "bin/ashs_main.sh",
'dirs': ["ext"] "bin/ashs_template_qsub.sh",
} "bin/ashs_train.sh",
"bin/ashs_util_makepdf.sh"],
'dirs': ["ext"]}
moduleclass = 'bio' moduleclass = 'bio'

7
a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb

@ -3,8 +3,8 @@ version = '3.10.2'
homepage = 'http://math-atlas.sourceforge.net' homepage = 'http://math-atlas.sourceforge.net'
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis
on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear
algebra kernel library.""" algebra kernel library."""
toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'}
@ -14,7 +14,8 @@ lapackver = '3.6.1'
versionsuffix = '-LAPACK-%s' % lapackver versionsuffix = '-LAPACK-%s' % lapackver
source_urls = [ source_urls = [
('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download'), ('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s',
'download'),
'http://www.netlib.org/lapack/', 'http://www.netlib.org/lapack/',
] ]
sources = [ sources = [

7
a/ATLAS/ATLAS-3.10.3-GCC-5.4.0-2.26-LAPACK-3.6.1.eb

@ -3,8 +3,8 @@ version = '3.10.3'
homepage = 'http://math-atlas.sourceforge.net' homepage = 'http://math-atlas.sourceforge.net'
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis
on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear
algebra kernel library.""" algebra kernel library."""
toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'}
@ -14,7 +14,8 @@ lapackver = '3.6.1'
versionsuffix = '-LAPACK-%s' % lapackver versionsuffix = '-LAPACK-%s' % lapackver
source_urls = [ source_urls = [
('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download'), ('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s',
'download'),
'http://www.netlib.org/lapack/', 'http://www.netlib.org/lapack/',
] ]
sources = [ sources = [

11
a/ATLAS/ATLAS-3.10.3-GCC-6.3.0-2.27-LAPACK-3.6.1.eb

@ -5,8 +5,8 @@ version = '3.10.3'
homepage = 'http://math-atlas.sourceforge.net' homepage = 'http://math-atlas.sourceforge.net'
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis
on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear
algebra kernel library.""" algebra kernel library."""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
@ -16,7 +16,8 @@ lapackver = '3.6.1'
versionsuffix = '-LAPACK-%s' % lapackver versionsuffix = '-LAPACK-%s' % lapackver
source_urls = [ source_urls = [
('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download'), ('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s',
'download'),
'http://www.netlib.org/lapack/', 'http://www.netlib.org/lapack/',
] ]
sources = [ sources = [
@ -32,11 +33,11 @@ configure_cmd_prefix = '.'
configopts = "-Ss f77lib '-L$(EBROOTGCC)/lib64 -lgfortran' " configopts = "-Ss f77lib '-L$(EBROOTGCC)/lib64 -lgfortran' "
# salomon # salomon
#configopts += '-b 64 -D c -DPentiumCPS=2500 ' #configopts += '-b 64 -D c -DPentiumCPS=2500 '
#anselm # anselm
configopts += '-b 64 -D c -DPentiumCPS=2300 ' configopts += '-b 64 -D c -DPentiumCPS=2300 '
configopts += '--with-netlib-lapack-tarfile=/apps/easybuild/sources/a/ATLAS/lapack-%s.tgz ' % lapackver configopts += '--with-netlib-lapack-tarfile=/apps/easybuild/sources/a/ATLAS/lapack-%s.tgz ' % lapackver
configopts += '-Fa alg -fPIC' configopts += '-Fa alg -fPIC'
prebuildopts = 'cd build && ' prebuildopts = 'cd build && '
preinstallopts = 'cd build && ' preinstallopts = 'cd build && '
preinstallopts += 'make check && ' preinstallopts += 'make check && '
#preinstallopts += 'make ptcheck && ' #preinstallopts += 'make ptcheck && '

6
a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb

@ -1,9 +1,11 @@
name = 'Amber' name = 'Amber'
version = '16' version = '16'
ambertools_ver = '16' ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html # Patch levels from http://ambermd.org/bugfixes16.html and
# http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber) patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1]) versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' % (
ambertools_ver, patchlevels[0], patchlevels[1])
homepage = 'http://ambermd.org/amber.html' homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy description = """Amber (originally Assisted Model Building with Energy

6
a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb

@ -1,9 +1,11 @@
name = 'Amber' name = 'Amber'
version = '16' version = '16'
ambertools_ver = '16' ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html # Patch levels from http://ambermd.org/bugfixes16.html and
# http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber) patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1]) versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (
ambertools_ver, patchlevels[0], patchlevels[1])
homepage = 'http://ambermd.org/amber.html' homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy description = """Amber (originally Assisted Model Building with Energy

6
a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb

@ -1,9 +1,11 @@
name = 'Amber' name = 'Amber'
version = '16' version = '16'
ambertools_ver = '16' ambertools_ver = '16'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html # Patch levels from http://ambermd.org/bugfixes16.html and
# http://ambermd.org/bugfixesat.html
patchlevels = (5, 14) # (AmberTools, Amber) patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1]) versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' % (
ambertools_ver, patchlevels[0], patchlevels[1])
homepage = 'http://ambermd.org/amber.html' homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy description = """Amber (originally Assisted Model Building with Energy

4
a/Amber/Amber-18-iomkl-2017b-AmberTools-18-serial.eb

@ -4,8 +4,8 @@ name = 'Amber'
version = '18' version = '18'
ambertools_ver = '18' ambertools_ver = '18'
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
#patchlevels = (5, 14) # (AmberTools, Amber) # patchlevels = (5, 14) # (AmberTools, Amber)
versionsuffix = '-AmberTools-%s-serial' %(ambertools_ver) versionsuffix = '-AmberTools-%s-serial' % (ambertools_ver)
homepage = 'http://ambermd.org/amber.html' homepage = 'http://ambermd.org/amber.html'
description = """Amber (originally Assisted Model Building with Energy description = """Amber (originally Assisted Model Building with Energy

10
a/AmberTools/AmberTools-15-intel-2015b-Python-2.7.11.eb

@ -20,21 +20,21 @@ toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '15' ambertools_ver = '15'
sources = [ sources = [
# 'Amber%(version)s.tar.bz2', # 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver, 'AmberTools%s.tar.bz2' % ambertools_ver,
] ]
configopts = '--no-updates' configopts = '--no-updates'
#patches = [ # patches = [
# 'Amber-%(version)s_fix-hardcoding.patch', # 'Amber-%(version)s_fix-hardcoding.patch',
# 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver, # 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
#] #]
dependencies = [ dependencies = [
# ('CUDA', '7.5.18', '', True), # ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'), # ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'), # ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'), ('Python', '2.7.11'),
] ]

13
a/AmberTools/AmberTools-16-intel-2015b-Python-2.7.11.eb

@ -13,24 +13,25 @@ toolchainopts = {'openmp': False, 'usempi': True}
ambertools_ver = '16' ambertools_ver = '16'
sources = [ sources = [
# 'Amber%(version)s.tar.bz2', # 'Amber%(version)s.tar.bz2',
'AmberTools%s.tar.bz2' % ambertools_ver, 'AmberTools%s.tar.bz2' % ambertools_ver,
] ]
patches = [ patches = [
# 'Amber-%(version)s_fix-hardcoding.patch', # 'Amber-%(version)s_fix-hardcoding.patch',
'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver, 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
] ]
dependencies = [ dependencies = [
# ('CUDA', '7.5.18', '', True), # ('CUDA', '7.5.18', '', True),
# ('netCDF', '4.4.0'), # ('netCDF', '4.4.0'),
# ('netCDF-Fortran', '4.4.4'), # ('netCDF-Fortran', '4.4.4'),
('Python', '2.7.11'), ('Python', '2.7.11'),
] ]
patchlevels = (13, 13) patchlevels = (13, 13)
patchruns = 1 patchruns = 1
versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (ambertools_ver, patchlevels[0], patchlevels[1]) versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (
ambertools_ver, patchlevels[0], patchlevels[1])
moduleclass = 'chem' moduleclass = 'chem'

12
a/Autoconf/Autoconf-2.69.eb

@ -18,8 +18,16 @@ sources = [SOURCELOWER_TAR_GZ]
dependencies = [('M4', '1.4.18')] dependencies = [('M4', '1.4.18')]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", 'files': [
"autoupdate", "ifnames"]], "bin/%s" %
x for x in [
"autoconf",
"autoheader",
"autom4te",
"autoreconf",
"autoscan",
"autoupdate",
"ifnames"]],
'dirs': [], 'dirs': [],
} }

10
a/almost/almost-2.1.0.eb

@ -22,11 +22,11 @@ source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
sources = [SOURCELOWER_TAR_GZ] sources = [SOURCELOWER_TAR_GZ]
builddependencies = [ builddependencies = [
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')), ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')), ('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
('SQLite', '3.8.8.1'), ('SQLite', '3.8.8.1'),
('gzip', '1.6'), ('gzip', '1.6'),
('Autotools', '20150215'), ('Autotools', '20150215'),
] ]
configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" ' configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '

2
a/angsd/angsd-0.910-foss-2016a.eb

@ -5,7 +5,7 @@ version = '0.910'
homepage = 'http://www.popgen.dk/angsd' homepage = 'http://www.popgen.dk/angsd'
description = """Program for analysing NGS data.""" description = """Program for analysing NGS data."""
toolchain = {'name': 'foss', 'version': '2016a'} toolchain = {'name': 'foss', 'version': '2016a'}
source_urls = ['https://github.com/ANGSD/angsd/archive/'] source_urls = ['https://github.com/ANGSD/angsd/archive/']

2
a/ant/ant-1.10.0-Java-1.8.0_112.eb

@ -1,6 +1,6 @@
name = 'ant' name = 'ant'
version = '1.10.0' version = '1.10.0'
versionsuffix = '-Java-%(javaver)s' versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/' homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files

2
a/ant/ant-1.9.7-Java-1.8.0_121.eb

@ -1,6 +1,6 @@
name = 'ant' name = 'ant'
version = '1.9.7' version = '1.9.7'
versionsuffix = '-Java-%(javaver)s' versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/' homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files

2
a/ant/ant-1.9.7-Java-1.8.0_92.eb

@ -1,6 +1,6 @@
name = 'ant' name = 'ant'
version = '1.9.7' version = '1.9.7'
versionsuffix = '-Java-%(javaver)s' versionsuffix = '-Java-%(javaver)s'
homepage = 'http://ant.apache.org/' homepage = 'http://ant.apache.org/'
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files

11
a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb

@ -22,8 +22,13 @@ patches = [
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = { sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT], 'files': [
'dirs': [] "lib/libarpack.a",
} "lib/libarpack.%s" %
SHLIB_EXT,
"lib/libparpack.a",
"lib/libparpack.%s" %
SHLIB_EXT],
'dirs': []}
moduleclass = 'numlib' moduleclass = 'numlib'

11
a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb

@ -22,8 +22,13 @@ patches = [
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
sanity_check_paths = { sanity_check_paths = {
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT], 'files': [
'dirs': [] "lib/libarpack.a",
} "lib/libarpack.%s" %
SHLIB_EXT,
"lib/libparpack.a",
"lib/libparpack.%s" %
SHLIB_EXT],
'dirs': []}
moduleclass = 'numlib' moduleclass = 'numlib'

2
a/asn1crypto/asn1crypto-0.24.0-Py-2.7.eb

@ -12,7 +12,7 @@ toolchain = {'name': 'Py', 'version': '2.7'}
source_urls = [PYPI_SOURCE] source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ] sources = [SOURCE_TAR_GZ]
#dependencies = [ # dependencies = [
# ('six', '1.11.0'), # ('six', '1.11.0'),
#] #]

2
a/astor/astor-0.6.2-Py-3.6.eb

@ -12,7 +12,7 @@ toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = [PYPI_SOURCE] source_urls = [PYPI_SOURCE]
sources = [SOURCE_TAR_GZ] sources = [SOURCE_TAR_GZ]
#dependencies = [ # dependencies = [
# ('MarkupSafe', '1.0'), # ('MarkupSafe', '1.0'),
#] #]

10
a/astroid/astroid-1.5.3-Python-2.7.13-base.eb

@ -8,8 +8,8 @@ versionsuffix = '-Python-2.7.13-base'
github_account = 'PyCQA' github_account = 'PyCQA'
homepage = 'https://github.com/PyCQA/astroid' homepage = 'https://github.com/PyCQA/astroid'
description = """The aim of this module is to provide a common base representation of python description = """The aim of this module is to provide a common base representation of python
source code for projects such as pychecker, pyreverse, pylint… Well, actually the development of source code for projects such as pychecker, pyreverse, pylint… Well, actually the development of
this library is essentially governed by pylint’s needs. It used to be called logilab-astng.""" this library is essentially governed by pylint’s needs. It used to be called logilab-astng."""
toolchain = {'name': 'dummy', 'version': ''} toolchain = {'name': 'dummy', 'version': ''}
@ -21,9 +21,7 @@ dependencies = [
('Python', '2.7.13', '-base', True), ('Python', '2.7.13', '-base', True),
] ]
sanity_check_paths = { sanity_check_paths = {'files': [], 'dirs': [
'files': [], 'lib/python%(pyshortver)s/site-packages/astroid-%(version)s-py2.7.egg'], }
'dirs': ['lib/python%(pyshortver)s/site-packages/astroid-%(version)s-py2.7.egg'],
}
moduleclass = 'lib' moduleclass = 'lib'

6
a/asv/asv-0.2.1-Py-2.7.eb

@ -16,9 +16,7 @@ dependencies = [
('six', '1.11.0'), ('six', '1.11.0'),
] ]
sanity_check_paths = { sanity_check_paths = {'files': [], 'dirs': [
'files': [], 'lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg'], }
'dirs': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg'],
}
moduleclass = 'python' moduleclass = 'python'

6
a/asv/asv-0.2.1-Py-3.6.eb

@ -16,9 +16,7 @@ dependencies = [
('six', '1.11.0'), ('six', '1.11.0'),
] ]
sanity_check_paths = { sanity_check_paths = {'files': [], 'dirs': [
'files': [], 'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg'], }
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg'],
}
moduleclass = 'python' moduleclass = 'python'

2
b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb

@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'foss', 'version': '2015b'} toolchain = {'name': 'foss', 'version': '2015b'}
source_urls = [SOURCEFORGE_SOURCE] source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz' ] sources = ['%(name)s_%(version)s.tar.gz']
java = 'Java' java = 'Java'
javaver = '1.8.0_66' javaver = '1.8.0_66'

2
b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb

@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'foss', 'version': '2015b'} toolchain = {'name': 'foss', 'version': '2015b'}
source_urls = [SOURCEFORGE_SOURCE] source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz' ] sources = ['%(name)s_%(version)s.tar.gz']
java = 'Java' java = 'Java'
javaver = '1.8.0_74' javaver = '1.8.0_74'

2
b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb

@ -10,7 +10,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
toolchain = {'name': 'intel', 'version': '2016b'} toolchain = {'name': 'intel', 'version': '2016b'}
source_urls = [SOURCEFORGE_SOURCE] source_urls = [SOURCEFORGE_SOURCE]
sources = ['%(name)s_%(version)s.tar.gz' ] sources = ['%(name)s_%(version)s.tar.gz']
dependencies = [('Java', '1.8.0_112', '', True)] dependencies = [('Java', '1.8.0_112', '', True)]

10
b/BCFtools/BCFtools-1.2-foss-2015a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
@ -32,7 +33,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

10
b/BCFtools/BCFtools-1.2-intel-2015a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
@ -32,7 +33,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

10
b/BCFtools/BCFtools-1.3-foss-2015g.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015g'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
dependencies = [ dependencies = [
('HTSlib', '1.3'), ('HTSlib', '1.3'),
@ -30,7 +31,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

10
b/BCFtools/BCFtools-1.3-foss-2016a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
@ -34,7 +35,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

10
b/BCFtools/BCFtools-1.3-intel-2016a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
@ -34,7 +35,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

15
b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -9,25 +9,26 @@ name = 'BCFtools'
version = '1.3.1' version = '1.3.1'
homepage = 'http://www.htslib.org/' homepage = 'http://www.htslib.org/'
description = """BCFtools is a set of utilities that manipulate variant calls in the description = """BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF""" Variant Call Format (VCF) and its binary counterpart BCF"""
toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchain = {'name': 'goolf', 'version': '1.7.20'}
source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] source_urls = [
'https://github.com/samtools/bcftools/releases/download/%(version)s/']
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
dependencies = [ dependencies = [
('zlib', '1.2.8'), ('zlib', '1.2.8'),
('GSL', '1.16'), ('GSL', '1.16'),
] ]
buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'"
runtest = 'test' runtest = 'test'
files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"),
"doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/bcftools"], 'files': ["bin/bcftools"],

10
b/BCFtools/BCFtools-1.6-intel-2017a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
#patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] #patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
@ -35,7 +36,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

10
b/BCFtools/BCFtools-1.8-intel-2017a.eb

@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] source_urls = [
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
#patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] #patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
@ -35,7 +36,12 @@ postinstallcmds = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], 'files': [
'bin/%s' %
x for x in [
'bcftools',
'plot-vcfstats',
'vcfutils.pl']],
'dirs': ['lib/plugins'], 'dirs': ['lib/plugins'],
} }

12
b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb

@ -9,9 +9,9 @@ name = "BEDOPS"
version = "2.4.1" version = "2.4.1"
homepage = 'https://github.com/bedops/bedops' homepage = 'https://github.com/bedops/bedops'
description = """ BEDOPS is an open-source command-line toolkit that performs highly description = """ BEDOPS is an open-source command-line toolkit that performs highly
efficient and scalable Boolean and other set operations, statistical calculations, efficient and scalable Boolean and other set operations, statistical calculations,
archiving, conversion and other management of genomic data of arbitrary scale.""" archiving, conversion and other management of genomic data of arbitrary scale."""
# this application requires GCC-4.8.x or higher # this application requires GCC-4.8.x or higher
# be aware if you switch to a different toolchain # be aware if you switch to a different toolchain
@ -27,9 +27,9 @@ parallel = 1
files_to_copy = ["bin"] files_to_copy = ["bin"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed",
"starchcat", "vcf2bed", "wig2bed", "starchcat", "vcf2bed", "wig2bed",
"gtf2bed", "bedops", "wig2bed"]], "gtf2bed", "bedops", "wig2bed"]],
'dirs': [] 'dirs': []
} }

3
b/BLAST/BLAST-2.2.26-Linux_x86_64.eb

@ -16,7 +16,8 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
toolchain = {'name': 'dummy', 'version': 'dummy'} toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/'] source_urls = [
'http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/']
sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz']
sanity_check_paths = { sanity_check_paths = {

28
b/BLAT/BLAT-3.5-goolf-1.4.10.eb

@ -22,11 +22,33 @@ dependencies = [('libpng', '1.6.2')]
buildopts = 'CC="$CC" COPT= L="$LIBS"' buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] files_to_copy = [
"bin",
"blat",
"gfClient",
"gfServer",
"hg",
"inc",
"jkOwnLib",
"lib",
"utils",
"webBlat"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', 'files': [
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], "bin/%s" %
x for x in [
'blat',
'faToNib',
'faToTwoBit',
'gfClient',
'gfServer',
'nibFrag',
'pslPretty',
'pslReps',
'pslSort',
'twoBitInfo',
'twoBitToFa']],
'dirs': files_to_copy, 'dirs': files_to_copy,
} }

28
b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb

@ -26,11 +26,33 @@ dependencies = [(libpng, libpng_ver)]
buildopts = 'CC="$CC" COPT= L="$LIBS"' buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] files_to_copy = [
"bin",
"blat",
"gfClient",
"gfServer",
"hg",
"inc",
"jkOwnLib",
"lib",
"utils",
"webBlat"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', 'files': [
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], "bin/%s" %
x for x in [
'blat',
'faToNib',
'faToTwoBit',
'gfClient',
'gfServer',
'nibFrag',
'pslPretty',
'pslReps',
'pslSort',
'twoBitInfo',
'twoBitToFa']],
'dirs': files_to_copy, 'dirs': files_to_copy,
} }

28
b/BLAT/BLAT-3.5-ictce-5.5.0.eb

@ -22,11 +22,33 @@ dependencies = [('libpng', '1.6.6')]
buildopts = 'CC="$CC" COPT= L="$LIBS"' buildopts = 'CC="$CC" COPT= L="$LIBS"'
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] files_to_copy = [
"bin",
"blat",
"gfClient",
"gfServer",
"hg",
"inc",
"jkOwnLib",
"lib",
"utils",
"webBlat"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', 'files': [
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], "bin/%s" %
x for x in [
'blat',
'faToNib',
'faToTwoBit',
'gfClient',
'gfServer',
'nibFrag',
'pslPretty',
'pslReps',
'pslSort',
'twoBitInfo',
'twoBitToFa']],
'dirs': files_to_copy, 'dirs': files_to_copy,
} }

9
b/BLCR/BLCR-0.8.5-GNU-5.1.0-2.25.eb

@ -4,16 +4,17 @@ name = 'BLCR'
version = '0.8.5' version = '0.8.5'
homepage = 'http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/' homepage = 'http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/'
description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers
are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide
a robust, production quality implementation that checkpoints a wide range of applications, a robust, production quality implementation that checkpoints a wide range of applications,
without requiring changes to be made to application code. """ without requiring changes to be made to application code. """
toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'}
toolchainopts = {'optarch': True, 'pic': True} toolchainopts = {'optarch': True, 'pic': True}
sources = [SOURCELOWER_TAR_GZ] sources = [SOURCELOWER_TAR_GZ]
source_urls = [('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')] source_urls = [
('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')]
sanity_check_paths = { sanity_check_paths = {
'files': ['include/libcr.h'], 'files': ['include/libcr.h'],

2
b/BWA/BWA-0.7.17-intel-2017a.eb

@ -12,7 +12,7 @@ source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
sources = [SOURCELOWER_TAR_BZ2] sources = [SOURCELOWER_TAR_BZ2]
dependencies = [ dependencies = [
('zlib', '1.2.11', '', True), ('zlib', '1.2.11', '', True),
] ]
moduleclass = 'bio' moduleclass = 'bio'

9
b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb

@ -8,10 +8,10 @@ name = 'BXH_XCEDE_TOOLS'
version = '1.11.1' version = '1.11.1'
homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/' homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/'
description = """A collection of data processing and image analysis description = """A collection of data processing and image analysis
tools for data in BXH or XCEDE format. This includes data format tools for data in BXH or XCEDE format. This includes data format
encapsulation/conversion, event-related analysis, QA tools, and more. encapsulation/conversion, event-related analysis, QA tools, and more.
These tools form the basis of the fBIRN QA procedures and are also These tools form the basis of the fBIRN QA procedures and are also
distributed as part of the fBIRN Data Upload Scripts.""" distributed as part of the fBIRN Data Upload Scripts."""
toolchain = {'name': 'dummy', 'version': 'dummy'} toolchain = {'name': 'dummy', 'version': 'dummy'}
@ -25,4 +25,3 @@ sanity_check_paths = {
} }
moduleclass = 'bio' moduleclass = 'bio'

4
b/Bash/Bash-4.2-intel-2015b.eb

@ -16,8 +16,8 @@ name = 'Bash'
version = '4.2' version = '4.2'
homepage = 'http://www.gnu.org/software/bash' homepage = 'http://www.gnu.org/software/bash'
description = """Bash is an sh-compatible command language interpreter that executes commands 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 read from the standard input or from a file. Bash also incorporates useful features from the
Korn and C shells (ksh and csh).""" Korn and C shells (ksh and csh)."""
toolchain = {'name': 'intel', 'version': '2015b'} toolchain = {'name': 'intel', 'version': '2015b'}

20
b/BayPass/BayPass-2.1-goolf-1.7.20.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -9,9 +9,9 @@ name = 'BayPass'
version = '2.1' version = '2.1'
homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html' homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html'
description = """BayPass is a population genomics software which is primarily aimed at identifying description = """BayPass is a population genomics software which is primarily aimed at identifying
genetic markers subjected to selection and/or associated to population-specific covariates genetic markers subjected to selection and/or associated to population-specific covariates
(e.g., environmental variables, quantitative or categorical phenotypic characteristics). (e.g., environmental variables, quantitative or categorical phenotypic characteristics).
The underlying models explicitly account for (and may estimate) the covariance structure among the The underlying models explicitly account for (and may estimate) the covariance structure among the
population allele frequencies that originates from the shared history of the populations under study""" population allele frequencies that originates from the shared history of the populations under study"""
@ -25,12 +25,12 @@ start_dir = 'sources'
parallel = 1 parallel = 1
files_to_copy = [(['sources/g_baypass'], 'bin/'), files_to_copy = [(['sources/g_baypass'], 'bin/'),
'BayPass_manual_2.1.pdf', 'BayPass_manual_2.1.pdf',
'examples', 'examples',
'Licence_CeCILL-B_V1-en.txt', 'Licence_CeCILL-B_V1-en.txt',
'utils' 'utils'
] ]
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/g_baypass'], 'files': ['bin/g_baypass'],

7
b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -20,10 +20,11 @@ sources = ['v%(version)s.tar.gz']
start_dir = 'source' start_dir = 'source'
files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] files_to_copy = [(['source/bayescenv'], 'bin'), 'test',
'COPYING', 'README.md', 'ChangeLog']
parallel = 1 parallel = 1
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/bayescenv'], 'files': ['bin/bayescenv'],
'dirs': [], 'dirs': [],

7
b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -19,10 +19,11 @@ sources = ['v%(version)s.tar.gz']
start_dir = 'source' start_dir = 'source'
files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] files_to_copy = [(['source/bayescenv'], 'bin'), 'test',
'COPYING', 'README.md', 'ChangeLog']
parallel = 1 parallel = 1
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/bayescenv'], 'files': ['bin/bayescenv'],
'dirs': [], 'dirs': [],

6
b/BayeScan/BayeScan-2.1-foss-2016a.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -9,7 +9,7 @@ name = 'BayeScan'
version = '2.1' version = '2.1'
homepage = 'http://cmpg.unibe.ch/software/BayeScan/' homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
using differences in allele frequencies between populations.""" using differences in allele frequencies between populations."""
toolchain = {'name': 'foss', 'version': '2016a'} toolchain = {'name': 'foss', 'version': '2016a'}
@ -30,7 +30,7 @@ files_to_copy = [
] ]
parallel = 1 parallel = 1
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/bayescan_%(version)s'], 'files': ['bin/bayescan_%(version)s'],
'dirs': [], 'dirs': [],

9
b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb

@ -1,7 +1,7 @@
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez # Author: Pablo Escobar Lopez
# sciCORE - University of Basel # sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics # SIB Swiss Institute of Bioinformatics
easyblock = 'MakeCp' easyblock = 'MakeCp'
@ -9,10 +9,11 @@ name = 'BayeScan'
version = '2.1' version = '2.1'
homepage = 'http://cmpg.unibe.ch/software/BayeScan/' homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
using differences in allele frequencies between populations.""" using differences in allele frequencies between populations."""
# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile # BayeScan makefile is hardcoded to use g++. In case you want to use a
# non-gcc toolchain you will need to patch the makefile
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
toolchainopts = {'openmp': True} toolchainopts = {'openmp': True}
@ -31,7 +32,7 @@ files_to_copy = [
'R functions'] 'R functions']
parallel = 1 parallel = 1
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/bayescan_%(version)s'], 'files': ['bin/bayescan_%(version)s'],
'dirs': [], 'dirs': [],

13
b/BayesAss/BayesAss-3.0.4-foss-2016a.eb

@ -4,24 +4,25 @@ name = 'BayesAss'
version = '3.0.4' version = '3.0.4'
homepage = 'http://www.rannala.org/?page_id=245' homepage = 'http://www.rannala.org/?page_id=245'
description = """ description = """
BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
""" """
toolchain = {'name': 'foss','version': '2016a'} toolchain = {'name': 'foss', 'version': '2016a'}
sources = ['BA3-%(version)s.tar.gz'] sources = ['BA3-%(version)s.tar.gz']
source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] source_urls = [
'http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/']
dependencies = [ dependencies = [
('GSL','2.1') ('GSL', '2.1')
] ]
runtest = 'check' runtest = 'check'
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/BA3'], 'files': ['bin/BA3'],
'dirs' : ['bin', 'include'] 'dirs': ['bin', 'include']
} }
moduleclass = 'bio' moduleclass = 'bio'

6
b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb

@ -1,4 +1,4 @@
# @author: Guilherme Peretti-Pezzi (CSCS) # @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp" easyblock = "CmdCp"
@ -6,7 +6,7 @@ name = 'Bazel'
version = '0.3.0' version = '0.3.0'
homepage = 'http://bazel.io/' homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably. description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software.""" It is used to build the majority of Google's software."""
toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchain = {'name': 'CrayGNU', 'version': '2016.03'}
@ -22,7 +22,7 @@ cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': ['bin'], 'dirs': ['bin'],
} }

11
b/Bazel/Bazel-0.4.4.eb

@ -1,5 +1,5 @@
# @author: Robert Schmidt (OHRI) # @author: Robert Schmidt (OHRI)
# @author: Guilherme Peretti-Pezzi (CSCS) # @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp" easyblock = "CmdCp"
@ -7,13 +7,14 @@ name = 'Bazel'
version = '0.4.4' version = '0.4.4'
homepage = 'http://bazel.io/' homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably. description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software.""" It is used to build the majority of Google's software."""
toolchain = {'name': 'dummy', 'version': 'dummy'} toolchain = {'name': 'dummy', 'version': 'dummy'}
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
dependencies = [ dependencies = [
('Java', '1.8.0_121'), ('Java', '1.8.0_121'),
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': [], 'dirs': [],
} }
moduleclass = 'devel' moduleclass = 'devel'

11
b/Bazel/Bazel-0.5.0-GCC-4.9.3-tf.eb

@ -1,5 +1,5 @@
# @author: Robert Schmidt (OHRI) # @author: Robert Schmidt (OHRI)
# @author: Guilherme Peretti-Pezzi (CSCS) # @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp" easyblock = "CmdCp"
@ -7,13 +7,14 @@ name = 'Bazel'
version = '0.5.0' version = '0.5.0'
homepage = 'http://bazel.io/' homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably. description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software.""" It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '4.9.3-tf'} toolchain = {'name': 'GCC', 'version': '4.9.3-tf'}
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
dependencies = [ dependencies = [
('Java', '1.8.0_121', '', True), ('Java', '1.8.0_121', '', True),
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': [], 'dirs': [],
} }
moduleclass = 'devel' moduleclass = 'devel'

11
b/Bazel/Bazel-0.5.0-GCC-7.1.0-2.28.eb

@ -1,5 +1,5 @@
# @author: Robert Schmidt (OHRI) # @author: Robert Schmidt (OHRI)
# @author: Guilherme Peretti-Pezzi (CSCS) # @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp" easyblock = "CmdCp"
@ -7,13 +7,14 @@ name = 'Bazel'
version = '0.5.0' version = '0.5.0'
homepage = 'http://bazel.io/' homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably. description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software.""" It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'} toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
dependencies = [ dependencies = [
('Java', '1.8.0_121', '', True), ('Java', '1.8.0_121', '', True),
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': [], 'dirs': [],
} }
moduleclass = 'devel' moduleclass = 'devel'

11
b/Bazel/Bazel-0.5.1-GCC-7.1.0-2.28.eb

@ -1,5 +1,5 @@
# @author: Robert Schmidt (OHRI) # @author: Robert Schmidt (OHRI)
# @author: Guilherme Peretti-Pezzi (CSCS) # @author: Guilherme Peretti-Pezzi (CSCS)
easyblock = "CmdCp" easyblock = "CmdCp"
@ -7,13 +7,14 @@ name = 'Bazel'
version = '0.5.1' version = '0.5.1'
homepage = 'http://bazel.io/' homepage = 'http://bazel.io/'
description = """Bazel is a build tool that builds code quickly and reliably. description = """Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software.""" It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'} toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
patches = [ patches = [
('cc_configure.patch'), ('cc_configure.patch'),
@ -30,9 +31,9 @@ cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': [], 'dirs': [],
} }
moduleclass = 'devel' moduleclass = 'devel'

7
b/Bazel/Bazel-0.5.4-GCC-7.1.0-2.28.eb

@ -13,7 +13,8 @@ It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'} toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
patches = [ patches = [
('cc_configure.patch'), ('cc_configure.patch'),
@ -30,9 +31,9 @@ cmds_map = [('.*', "./compile.sh")]
files_to_copy = [(['output/bazel'], 'bin')] files_to_copy = [(['output/bazel'], 'bin')]
sanity_check_paths={ sanity_check_paths = {
'files': ['bin/bazel'], 'files': ['bin/bazel'],
'dirs': [], 'dirs': [],
} }
moduleclass = 'devel' moduleclass = 'devel'

3
b/Bazel/Bazel-0.7.0-GCC-6.3.0-2.27.eb

@ -7,7 +7,8 @@ It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416'] checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416']

3
b/Bazel/Bazel-0.7.0-GCC-7.1.0-2.28.eb

@ -7,7 +7,8 @@ It is used to build the majority of Google's software."""
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'} toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] source_urls = [
'https://github.com/bazelbuild/bazel/releases/download/%(version)s']
sources = ['%(namelower)s-%(version)s-dist.zip'] sources = ['%(namelower)s-%(version)s-dist.zip']
checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416'] checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416']

13
b/Beast/Beast-1.8.4.eb

@ -9,16 +9,17 @@ name = 'Beast'
version = '1.8.4' version = '1.8.4'
homepage = 'http://beast.bio.ed.ac.uk/' homepage = 'http://beast.bio.ed.ac.uk/'
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
but is also a framework for testing evolutionary hypotheses without conditioning on a single but is also a framework for testing evolutionary hypotheses without conditioning on a single
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
proportional to its posterior probability. """ proportional to its posterior probability. """
toolchain = {'name': 'dummy', 'version': ''} toolchain = {'name': 'dummy', 'version': ''}
source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] source_urls = [
'https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/']
sources = ['BEASTv%(version)s.tgz'] sources = ['BEASTv%(version)s.tgz']
dependencies = [ dependencies = [

2
b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb

@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
installopts = 'INSTDIR=%(installdir)s' installopts = 'INSTDIR=%(installdir)s'
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/'+prog+'.'+flavor+'.x' 'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']], for flavor in ['real', 'cplx']],
'dirs': [] 'dirs': []

2
b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb

@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
installopts = 'INSTDIR=%(installdir)s' installopts = 'INSTDIR=%(installdir)s'
sanity_check_paths = { sanity_check_paths = {
'files': ['bin/'+prog+'.'+flavor+'.x' 'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']], for flavor in ['real', 'cplx']],
'dirs': [] 'dirs': []

8
b/BerkeleyUPC/BerkeleyUPC-2.16.2-gompi-2015b.eb

@ -4,9 +4,9 @@ name = 'BerkeleyUPC'
version = '2.16.2' version = '2.16.2'
homepage = 'http://upc.lbl.gov' homepage = 'http://upc.lbl.gov'
description = """The goal of the Berkeley UPC compiler group is to develop a portable, description = """The goal of the Berkeley UPC compiler group is to develop a portable,
high performance implementation of UPC for large-scale multiprocessors, PC clusters, high performance implementation of UPC for large-scale multiprocessors, PC clusters,
and clusters of shared memory multiprocessors. and clusters of shared memory multiprocessors.
""" """
toolchain = {'name': 'gompi', 'version': '2015b'} toolchain = {'name': 'gompi', 'version': '2015b'}
@ -19,7 +19,7 @@ sources = ['berkeley_upc-%(version)s.tar.gz']
preconfigopts = './Bootstrap -L && ' preconfigopts = './Bootstrap -L && '
preconfigopts += 'export CFLAGS="$OPTFLAGS -fopenmp -Wl,-rpath,$EBROOTGCC/lib64" && ' preconfigopts += 'export CFLAGS="$OPTFLAGS -fopenmp -Wl,-rpath,$EBROOTGCC/lib64" && '
# Manually create build directory # Manually create build directory
preconfigopts += 'mkdir build && cd build && ' preconfigopts += 'mkdir build && cd build && '
# To be able run "../configure" # To be able run "../configure"
configure_cmd_prefix = "." configure_cmd_prefix = "."

5
b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb

@ -27,8 +27,8 @@ exts_list = [
}), }),
(name, version, { (name, version, {
'modulename': 'Bio::Perl', 'modulename': 'Bio::Perl',
'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'),
'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'],
}), }),
] ]
@ -37,4 +37,3 @@ modextrapaths = {
} }
moduleclass = 'bio' moduleclass = 'bio'

10
b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb

@ -34,11 +34,11 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [], 'dirs': [
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, 'lib/python%s/site-packages/Bio' %
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver), pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' %
'lib/python%s/site-packages/BioSQL' % pyshortver] (pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' %
} pyshortver]}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

10
b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb

@ -34,11 +34,11 @@ dependencies = [
] ]
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [], 'dirs': [
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver, 'lib/python%s/site-packages/Bio' %
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver), pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' %
'lib/python%s/site-packages/BioSQL' % pyshortver] (pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' %
} pyshortver]}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

5
b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb

@ -29,8 +29,9 @@ dependencies = [
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [],
'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] 'dirs': [
} 'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

5
b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb

@ -33,8 +33,9 @@ dependencies = [
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [],
'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] 'dirs': [
} 'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

5
b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb

@ -29,8 +29,9 @@ dependencies = [
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [],
'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] 'dirs': [
} 'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

5
b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb

@ -29,8 +29,9 @@ dependencies = [
sanity_check_paths = { sanity_check_paths = {
'files': [], 'files': [],
'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] 'dirs': [
} 'lib/python%(pyshortver)s/site-packages/Bio',
'lib/python%(pyshortver)s/site-packages/BioSQL']}
options = {'modulename': 'Bio'} options = {'modulename': 'Bio'}

6
b/BoltzTraP2/BoltzTraP2-18.1.1-Py-3.6.eb

@ -28,9 +28,7 @@ builddependencies = [
options = {'modulename': 'BoltzTraP2'} options = {'modulename': 'BoltzTraP2'}
sanity_check_paths = { sanity_check_paths = {'files': [], 'dirs': [
'files': [], 'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'], }
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'],
}
moduleclass = 'python' moduleclass = 'python'

6
b/BoltzTraP2/BoltzTraP2-18.1.2-Py-3.6.eb

@ -28,9 +28,7 @@ builddependencies = [
options = {'modulename': 'BoltzTraP2'} options = {'modulename': 'BoltzTraP2'}
sanity_check_paths = { sanity_check_paths = {'files': [], 'dirs': [
'files': [], 'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'], }
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'],
}
moduleclass = 'python' moduleclass = 'python'

2
b/Boost/Boost-1.49.0-goolf-1.5.16-Python-2.7.3.eb

@ -21,6 +21,6 @@ dependencies = [
# also build boost_mpi # also build boost_mpi
boost_mpi = True boost_mpi = True
osdependencies = [('zlib-devel','zlib1g-dev')] osdependencies = [('zlib-devel', 'zlib1g-dev')]
moduleclass = 'devel' moduleclass = 'devel'

2
b/Boost/Boost-1.58.0-gompi-2015e-Python-2.7.9.eb

@ -4,7 +4,7 @@ version = '1.58.0'
homepage = 'http://www.boost.org/' homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries.""" description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'gompi', 'version': '2015e'} toolchain = {'name': 'gompi', 'version': '2015e'}
toolchainopts = {'pic': True, 'usempi': True} toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE] source_urls = [SOURCEFORGE_SOURCE]

4
b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb

@ -18,13 +18,13 @@ pythonversion = '2.7.11'
versionsuffix = '-Python-%s' % pythonversion versionsuffix = '-Python-%s' % pythonversion
dependencies = [ dependencies = [
('bzip2', '1.0.6' ), ('bzip2', '1.0.6'),
('Python', pythonversion), ('Python', pythonversion),
] ]
# also build boost_mpi # also build boost_mpi
boost_mpi = True boost_mpi = True
osdependencies = [('zlib-devel','zlib1g-dev')] osdependencies = [('zlib-devel', 'zlib1g-dev')]
moduleclass = 'devel' moduleclass = 'devel'

12
b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb

@ -9,16 +9,18 @@ name = 'Bowtie2'
version = '2.0.5' version = '2.0.5'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),

12
b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb

@ -9,16 +9,18 @@ name = 'Bowtie2'
version = '2.0.6' version = '2.0.6'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),

12
b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb

@ -9,16 +9,18 @@ name = 'Bowtie2'
version = '2.1.0' version = '2.1.0'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),

34
b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb

@ -9,24 +9,38 @@ name = 'Bowtie2'
version = '2.2.0' version = '2.2.0'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [(["bowtie2",
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", "bowtie2-align-l",
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "bowtie2-align-s",
"doc", "example", "scripts"] "bowtie2-build",
"bowtie2-build-l",
"bowtie2-build-s",
"bowtie2-inspect",
"bowtie2-inspect-l",
"bowtie2-inspect-s"],
'bin'),
"doc",
"example",
"scripts"]
sanity_check_paths = { sanity_check_paths = {
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [], 'dirs': [],
} }

37
b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb

@ -9,24 +9,41 @@ name = 'Bowtie2'
version = '2.2.2' version = '2.2.2'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [(["bowtie2",
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", "bowtie2-align-l",
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "bowtie2-align-s",
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] "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 = { sanity_check_paths = {
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [], 'dirs': [],
} }

37
b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb

@ -11,24 +11,41 @@ name = 'Bowtie2'
version = '2.2.4' version = '2.2.4'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [(["bowtie2",
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", "bowtie2-align-l",
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "bowtie2-align-s",
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] "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 = { sanity_check_paths = {
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [], 'dirs': [],
} }

37
b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb

@ -11,24 +11,41 @@ name = 'Bowtie2'
version = '2.2.5' version = '2.2.5'
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 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 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. 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, 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.""" its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchain = {'name': 'goolf', 'version': '1.7.20'}
sources = ['%(namelower)s-%(version)s-source.zip'] sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] source_urls = [
('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s',
'download')]
files_to_copy = [ files_to_copy = [(["bowtie2",
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", "bowtie2-align-l",
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), "bowtie2-align-s",
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] "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 = { sanity_check_paths = {
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'files': [
"bin/bowtie2-align-l",
"bin/bowtie2-build",
"bin/bowtie2-inspect"],
'dirs': [], 'dirs': [],
} }

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