mirror of
https://code.it4i.cz/sccs/easyconfigs-it4i.git
synced 2025-04-04 06:11:36 +01:00
formatter
This commit is contained in:
Lukáš Krupčík
parent
e3338cde79
commit
92cb0848fe
@ -17,14 +17,14 @@ toolchain = {'name': 'foss', 'version': '2015b'}
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sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
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source_urls = ['http://ftp.abinit.org/']
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#sanity_check_paths = {
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# 'files': ["bin/abinit"],
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# sanity_check_paths = {
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# 'files': ["bin/abinit"],
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# 'dirs': []
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# }
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moduleclass = 'chem'
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configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
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''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
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''' --enable-debug="no" ''' + \
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''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
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''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
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''' --enable-debug="no" ''' + \
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''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
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@ -18,15 +18,14 @@ toolchain = {'name': 'goolf', 'version': '1.5.16'}
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sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
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source_urls = ['http://ftp.abinit.org/']
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#sanity_check_paths = {
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# 'files': ["bin/abinit"],
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# sanity_check_paths = {
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# 'files': ["bin/abinit"],
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# 'dirs': []
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# }
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moduleclass = 'chem'
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configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
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''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
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''' --enable-debug="no" ''' + \
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''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
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''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
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''' --enable-debug="no" ''' + \
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''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
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@ -26,7 +26,16 @@ dependencies = [
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]
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sanity_check_paths = {
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'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
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'files': [
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'bin/%s' %
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x for x in [
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'abinit',
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'aim',
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'cut3d',
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'conducti',
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'mrgddb',
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'mrgscr',
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'optic']],
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'dirs': ['lib/pkgconfig'],
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}
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@ -21,12 +21,21 @@ configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$
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dependencies = [
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('libxc', '4.0.2'),
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# ('netCDF', '4.4.1.1'),
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# ('netCDF-Fortran', '4.4.4'),
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# ('netCDF', '4.4.1.1'),
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# ('netCDF-Fortran', '4.4.4'),
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]
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sanity_check_paths = {
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'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
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'files': [
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'bin/%s' %
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x for x in [
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'abinit',
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'aim',
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'cut3d',
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'conducti',
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'mrgddb',
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'mrgscr',
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'optic']],
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'dirs': ['lib/pkgconfig'],
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}
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@ -23,8 +23,16 @@ files_to_copy = [
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]
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sanity_check_paths = {
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'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a',
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'COPYRIGHT', 'manual.html', 'prims.gif', 'README'],
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'files': [
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'bin/tctest',
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'bin/tctest2',
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'bin/tcsample',
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'include/ac/tc.h',
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'lib/libactc.a',
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'COPYRIGHT',
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'manual.html',
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'prims.gif',
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'README'],
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'dirs': [],
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}
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@ -4,10 +4,10 @@ name = 'ALAMODE'
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version = '0.9.8'
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homepage = 'http://alamode.readthedocs.io/'
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description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity
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and lattice thermal conductivity of solids. By using an external DFT package such as VASP and
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Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly
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with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice
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description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity
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and lattice thermal conductivity of solids. By using an external DFT package such as VASP and
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Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly
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with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice
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thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles."""
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toolchain = {'name': 'intel', 'version': '2017a'}
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@ -16,10 +16,10 @@ source_urls = [SOURCEFORGE_SOURCE]
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sources = [SOURCELOWER_TAR_GZ]
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dependencies = [
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('Boost', '1.63.0'),
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('Python', '2.7.13-base', '', True),
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('matplotlib', '2.0.2-Python-2.7.13-base', '', True),
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('numpy', '1.13.0-Python-2.7.13-base', '', True),
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('Boost', '1.63.0'),
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('Python', '2.7.13-base', '', True),
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('matplotlib', '2.0.2-Python-2.7.13-base', '', True),
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('numpy', '1.13.0-Python-2.7.13-base', '', True),
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]
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commands = "cd alm && mv Makefile.linux Makefile && make && cd .. && "
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@ -29,9 +29,9 @@ commands += "cd tools && make "
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cmds_map = [('.*', commands)]
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files_to_copy = [
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(['alm/alm', 'anphon/anphon'], 'bin'),
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(['tools/analyze_phonons', 'tools/qe2alm'], 'tools'),
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(['tools/*.py'], 'tools'),
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(['alm/alm', 'anphon/anphon'], 'bin'),
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(['tools/analyze_phonons', 'tools/qe2alm'], 'tools'),
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(['tools/*.py'], 'tools'),
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]
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modextrapaths = {'PATH': 'tools'}
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@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s'
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homepage = "http://alps.comp-phys.org/"
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description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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C++ libraries for simplifying the development of such code.
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"""
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@ -32,7 +32,7 @@ modextrapaths = {
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'PYTHONPATH': ['lib/']
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}
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sanity_check_paths={
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sanity_check_paths = {
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'files': ['lib/libalps.%s' % SHLIB_EXT],
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'dirs': ['include/alps', 'bin/', 'share/'],
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}
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@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s'
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homepage = "http://alps.comp-phys.org/"
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description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as
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C++ libraries for simplifying the development of such code.
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"""
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@ -32,7 +32,7 @@ modextrapaths = {
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'PYTHONPATH': ['lib/']
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}
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sanity_check_paths={
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sanity_check_paths = {
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'files': ['lib/libalps.%s' % SHLIB_EXT],
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'dirs': ['include/alps', 'bin/', 'share/'],
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}
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@ -29,9 +29,18 @@ modextravars = {
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'ALPS_ROOT': '$root',
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}
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sanity_check_paths={
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'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'],
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'dirs': ['include/alps', 'lib/', 'share/'],
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sanity_check_paths = {
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'files': [
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'lib/libalps-accumulators.so',
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'lib/libalps-gf.so',
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'lib/libalps-hdf5.so',
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'lib/libalps-mc.so',
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'lib/libalps-params.so',
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'lib/libalps-utilities.so'],
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'dirs': [
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'include/alps',
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'lib/',
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'share/'],
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}
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moduleclass = 'phys'
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@ -4,8 +4,8 @@ name = 'ANSYS'
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version = '18.0'
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homepage = 'http://www.ansys.com'
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description = """ANSYS simulation software enables organizations to confidently predict
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how their products will operate in the real world. We believe that every product is
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description = """ANSYS simulation software enables organizations to confidently predict
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how their products will operate in the real world. We believe that every product is
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a promise of something greater. """
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toolchain = {'name': 'intel', 'version': '2017a'}
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@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
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sources = ['ANSYS-18.0.zip']
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dependencies = [
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('libpng', '1.2.59', '', True)
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('libpng', '1.2.59', '', True)
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]
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import os
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@ -4,8 +4,8 @@ name = 'ANSYS'
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version = '18.0'
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homepage = 'http://www.ansys.com'
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description = """ANSYS simulation software enables organizations to confidently predict
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how their products will operate in the real world. We believe that every product is
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description = """ANSYS simulation software enables organizations to confidently predict
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how their products will operate in the real world. We believe that every product is
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a promise of something greater. """
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toolchain = {'name': 'dummy', 'version': ''}
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@ -15,7 +15,7 @@ toolchain = {'name': 'dummy', 'version': ''}
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sources = ['ANSYS-18.0.zip']
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dependencies = [
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('libpng', '1.2.59', '', True)
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('libpng', '1.2.59', '', True)
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]
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import os
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@ -15,8 +15,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
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sources = ['ANSYS-18.2.zip']
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dependencies = [
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('libpng', '1.2.59', '', True),
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# ('libX11', '1.6.3', '', True),
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('libpng', '1.2.59', '', True),
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# ('libX11', '1.6.3', '', True),
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]
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import os
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@ -16,12 +16,12 @@ toolchain = {'name': 'intel', 'version': '2017b'}
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sources = ['ANSYS-19.0.zip']
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dependencies = [
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# ('libpng', '1.2.59', '', True),
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# ('libXrender', '0.9.9', '', True),
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('X11', '20170314', '', True),
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# ('libpng', '1.2.59', '', True),
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# ('libXrender', '0.9.9', '', True),
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('X11', '20170314', '', True),
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]
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#modextrapaths = {
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# modextrapaths = {
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# 'LD_LIBRARY_PATH': ['$LD_LIBRARY_PATH:%(installdir)s/v190/Electronics/Linux64/defer:%(installdir)s/v190/Framework/bin/Linux64'],
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# 'LD_LIBRARY_PATH': 'v190/Electronics/Linux64/defer',
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# 'LD_LIBRARY_PATH': 'v190/Framework/bin/Linux64',
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@ -20,7 +20,11 @@ dependencies = [
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configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT "
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sanity_check_paths = {
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'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"],
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'files': [
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"bin/apu-1-config",
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"lib/libaprutil-1.%s" %
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SHLIB_EXT,
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"lib/libaprutil-1.a"],
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'dirs': ["include/apr-1"],
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}
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@ -12,7 +12,11 @@ source_urls = ['http://archive.apache.org/dist/apr/']
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sources = [SOURCELOWER_TAR_GZ]
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sanity_check_paths = {
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'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"],
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'files': [
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"bin/apr-1-config",
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"lib/libapr-1.%s" %
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SHLIB_EXT,
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"lib/libapr-1.a"],
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'dirs': ["include/apr-1"],
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}
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@ -23,7 +23,12 @@ dependencies = [
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]
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sanity_check_paths = {
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'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
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'files': [
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'bin/ase-build',
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'bin/ase-db',
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'bin/ase-gui',
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'bin/ase-info',
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'bin/ase-run'],
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'dirs': ['lib/python3.6/site-packages'],
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}
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@ -18,13 +18,18 @@ checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
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dependencies = [
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('Python', '2.7.13'),
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# ('numpy', '1.13.0', '-Python-2.7.13-base'),
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# ('scipy', '0.19.1', '-Python-2.7.13-base'),
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# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
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# ('numpy', '1.13.0', '-Python-2.7.13-base'),
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# ('scipy', '0.19.1', '-Python-2.7.13-base'),
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# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
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]
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sanity_check_paths = {
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'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
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'files': [
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'bin/ase-build',
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'bin/ase-db',
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'bin/ase-gui',
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'bin/ase-info',
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'bin/ase-run'],
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'dirs': ['lib/python%(pyshortver)s/site-packages'],
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}
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@ -24,7 +24,12 @@ dependencies = [
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]
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sanity_check_paths = {
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'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
|
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'files': [
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'bin/ase-build',
|
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'bin/ase-db',
|
||||
'bin/ase-gui',
|
||||
'bin/ase-info',
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||||
'bin/ase-run'],
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'dirs': ['lib/python%(pyshortver)s/site-packages'],
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}
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@ -18,13 +18,18 @@ checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
|
||||
|
||||
dependencies = [
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||||
('Python', '3.6.1'),
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# ('numpy', '1.13.0', '-Python-2.7.13-base'),
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# ('scipy', '0.19.1', '-Python-2.7.13-base'),
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# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
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# ('numpy', '1.13.0', '-Python-2.7.13-base'),
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# ('scipy', '0.19.1', '-Python-2.7.13-base'),
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# ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
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]
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sanity_check_paths = {
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'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
|
||||
'files': [
|
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'bin/ase-build',
|
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'bin/ase-db',
|
||||
'bin/ase-gui',
|
||||
'bin/ase-info',
|
||||
'bin/ase-run'],
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'dirs': ['lib/python%(pyshortver)s/site-packages'],
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}
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@ -22,7 +22,12 @@ dependencies = [
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||||
]
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||||
|
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sanity_check_paths = {
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'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
|
||||
'files': [
|
||||
'bin/ase-build',
|
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'bin/ase-db',
|
||||
'bin/ase-gui',
|
||||
'bin/ase-info',
|
||||
'bin/ase-run'],
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'dirs': ['lib/python%(pyshortver)s/site-packages'],
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||||
}
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||||
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||||
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@ -12,18 +12,20 @@ description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """
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||||
toolchain = {'name': 'dummy', 'version': 'dummy'}
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||||
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||||
#You need to create an account to download the source
|
||||
#from https://www.nitrc.org/frs/?group_id=370
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# You need to create an account to download the source
|
||||
# from https://www.nitrc.org/frs/?group_id=370
|
||||
sources = ['ashs_Linux64_%(version)s.tgz']
|
||||
|
||||
checksums= ["07fea2883b856af8797b200212b72e71"]
|
||||
checksums = ["07fea2883b856af8797b200212b72e71"]
|
||||
|
||||
modextravars = {'ASHS_ROOT': '%(installdir)s'}
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh",
|
||||
"bin/ashs_util_makepdf.sh"],
|
||||
'dirs': ["ext"]
|
||||
}
|
||||
'files': [
|
||||
"bin/ashs_main.sh",
|
||||
"bin/ashs_template_qsub.sh",
|
||||
"bin/ashs_train.sh",
|
||||
"bin/ashs_util_makepdf.sh"],
|
||||
'dirs': ["ext"]}
|
||||
|
||||
moduleclass = 'bio'
|
||||
|
||||
@ -3,8 +3,8 @@ version = '3.10.2'
|
||||
|
||||
homepage = 'http://math-atlas.sourceforge.net'
|
||||
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
|
||||
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
|
||||
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
|
||||
algebra kernel library."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'}
|
||||
@ -14,7 +14,8 @@ lapackver = '3.6.1'
|
||||
versionsuffix = '-LAPACK-%s' % lapackver
|
||||
|
||||
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/',
|
||||
]
|
||||
sources = [
|
||||
|
||||
@ -3,8 +3,8 @@ version = '3.10.3'
|
||||
|
||||
homepage = 'http://math-atlas.sourceforge.net'
|
||||
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
|
||||
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
|
||||
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
|
||||
algebra kernel library."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'}
|
||||
@ -14,7 +14,8 @@ lapackver = '3.6.1'
|
||||
versionsuffix = '-LAPACK-%s' % lapackver
|
||||
|
||||
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/',
|
||||
]
|
||||
sources = [
|
||||
|
||||
@ -5,8 +5,8 @@ version = '3.10.3'
|
||||
|
||||
homepage = 'http://math-atlas.sourceforge.net'
|
||||
description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of
|
||||
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
|
||||
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
|
||||
algebra kernel library."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
|
||||
@ -16,7 +16,8 @@ lapackver = '3.6.1'
|
||||
versionsuffix = '-LAPACK-%s' % lapackver
|
||||
|
||||
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/',
|
||||
]
|
||||
sources = [
|
||||
@ -32,11 +33,11 @@ configure_cmd_prefix = '.'
|
||||
configopts = "-Ss f77lib '-L$(EBROOTGCC)/lib64 -lgfortran' "
|
||||
# salomon
|
||||
#configopts += '-b 64 -D c -DPentiumCPS=2500 '
|
||||
#anselm
|
||||
# anselm
|
||||
configopts += '-b 64 -D c -DPentiumCPS=2300 '
|
||||
configopts += '--with-netlib-lapack-tarfile=/apps/easybuild/sources/a/ATLAS/lapack-%s.tgz ' % lapackver
|
||||
configopts += '-Fa alg -fPIC'
|
||||
prebuildopts = 'cd build && '
|
||||
prebuildopts = 'cd build && '
|
||||
preinstallopts = 'cd build && '
|
||||
preinstallopts += 'make check && '
|
||||
#preinstallopts += 'make ptcheck && '
|
||||
|
||||
@ -1,9 +1,11 @@
|
||||
name = 'Amber'
|
||||
version = '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)
|
||||
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'
|
||||
description = """Amber (originally Assisted Model Building with Energy
|
||||
|
||||
@ -1,9 +1,11 @@
|
||||
name = 'Amber'
|
||||
version = '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)
|
||||
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'
|
||||
description = """Amber (originally Assisted Model Building with Energy
|
||||
|
||||
@ -1,9 +1,11 @@
|
||||
name = 'Amber'
|
||||
version = '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)
|
||||
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'
|
||||
description = """Amber (originally Assisted Model Building with Energy
|
||||
|
||||
@ -4,8 +4,8 @@ name = 'Amber'
|
||||
version = '18'
|
||||
ambertools_ver = '18'
|
||||
# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
|
||||
#patchlevels = (5, 14) # (AmberTools, Amber)
|
||||
versionsuffix = '-AmberTools-%s-serial' %(ambertools_ver)
|
||||
# patchlevels = (5, 14) # (AmberTools, Amber)
|
||||
versionsuffix = '-AmberTools-%s-serial' % (ambertools_ver)
|
||||
|
||||
homepage = 'http://ambermd.org/amber.html'
|
||||
description = """Amber (originally Assisted Model Building with Energy
|
||||
|
||||
@ -20,21 +20,21 @@ toolchainopts = {'openmp': False, 'usempi': True}
|
||||
|
||||
ambertools_ver = '15'
|
||||
sources = [
|
||||
# 'Amber%(version)s.tar.bz2',
|
||||
# 'Amber%(version)s.tar.bz2',
|
||||
'AmberTools%s.tar.bz2' % ambertools_ver,
|
||||
]
|
||||
|
||||
configopts = '--no-updates'
|
||||
|
||||
#patches = [
|
||||
# patches = [
|
||||
# 'Amber-%(version)s_fix-hardcoding.patch',
|
||||
# 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
|
||||
#]
|
||||
|
||||
dependencies = [
|
||||
# ('CUDA', '7.5.18', '', True),
|
||||
# ('netCDF', '4.4.0'),
|
||||
# ('netCDF-Fortran', '4.4.4'),
|
||||
# ('CUDA', '7.5.18', '', True),
|
||||
# ('netCDF', '4.4.0'),
|
||||
# ('netCDF-Fortran', '4.4.4'),
|
||||
('Python', '2.7.11'),
|
||||
]
|
||||
|
||||
|
||||
@ -13,24 +13,25 @@ toolchainopts = {'openmp': False, 'usempi': True}
|
||||
|
||||
ambertools_ver = '16'
|
||||
sources = [
|
||||
# 'Amber%(version)s.tar.bz2',
|
||||
# 'Amber%(version)s.tar.bz2',
|
||||
'AmberTools%s.tar.bz2' % ambertools_ver,
|
||||
]
|
||||
patches = [
|
||||
# 'Amber-%(version)s_fix-hardcoding.patch',
|
||||
# 'Amber-%(version)s_fix-hardcoding.patch',
|
||||
'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
|
||||
]
|
||||
|
||||
dependencies = [
|
||||
# ('CUDA', '7.5.18', '', True),
|
||||
# ('netCDF', '4.4.0'),
|
||||
# ('netCDF-Fortran', '4.4.4'),
|
||||
# ('CUDA', '7.5.18', '', True),
|
||||
# ('netCDF', '4.4.0'),
|
||||
# ('netCDF-Fortran', '4.4.4'),
|
||||
('Python', '2.7.11'),
|
||||
]
|
||||
|
||||
patchlevels = (13, 13)
|
||||
patchruns = 1
|
||||
|
||||
versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (ambertools_ver, patchlevels[0], patchlevels[1])
|
||||
versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (
|
||||
ambertools_ver, patchlevels[0], patchlevels[1])
|
||||
|
||||
moduleclass = 'chem'
|
||||
|
||||
@ -18,8 +18,16 @@ sources = [SOURCELOWER_TAR_GZ]
|
||||
dependencies = [('M4', '1.4.18')]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
|
||||
"autoupdate", "ifnames"]],
|
||||
'files': [
|
||||
"bin/%s" %
|
||||
x for x in [
|
||||
"autoconf",
|
||||
"autoheader",
|
||||
"autom4te",
|
||||
"autoreconf",
|
||||
"autoscan",
|
||||
"autoupdate",
|
||||
"ifnames"]],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
|
||||
@ -22,11 +22,11 @@ source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
|
||||
builddependencies = [
|
||||
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
|
||||
('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
|
||||
('SQLite', '3.8.8.1'),
|
||||
('gzip', '1.6'),
|
||||
('Autotools', '20150215'),
|
||||
('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
|
||||
('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
|
||||
('SQLite', '3.8.8.1'),
|
||||
('gzip', '1.6'),
|
||||
('Autotools', '20150215'),
|
||||
]
|
||||
|
||||
configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
|
||||
|
||||
@ -5,7 +5,7 @@ version = '0.910'
|
||||
|
||||
homepage = 'http://www.popgen.dk/angsd'
|
||||
description = """Program for analysing NGS data."""
|
||||
|
||||
|
||||
toolchain = {'name': 'foss', 'version': '2016a'}
|
||||
|
||||
source_urls = ['https://github.com/ANGSD/angsd/archive/']
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
name = 'ant'
|
||||
version = '1.10.0'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
|
||||
homepage = 'http://ant.apache.org/'
|
||||
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
name = 'ant'
|
||||
version = '1.9.7'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
|
||||
homepage = 'http://ant.apache.org/'
|
||||
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
name = 'ant'
|
||||
version = '1.9.7'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
versionsuffix = '-Java-%(javaver)s'
|
||||
|
||||
homepage = 'http://ant.apache.org/'
|
||||
description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
|
||||
|
||||
@ -22,8 +22,13 @@ patches = [
|
||||
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
|
||||
'dirs': []
|
||||
}
|
||||
'files': [
|
||||
"lib/libarpack.a",
|
||||
"lib/libarpack.%s" %
|
||||
SHLIB_EXT,
|
||||
"lib/libparpack.a",
|
||||
"lib/libparpack.%s" %
|
||||
SHLIB_EXT],
|
||||
'dirs': []}
|
||||
|
||||
moduleclass = 'numlib'
|
||||
|
||||
@ -22,8 +22,13 @@ patches = [
|
||||
configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
|
||||
'dirs': []
|
||||
}
|
||||
'files': [
|
||||
"lib/libarpack.a",
|
||||
"lib/libarpack.%s" %
|
||||
SHLIB_EXT,
|
||||
"lib/libparpack.a",
|
||||
"lib/libparpack.%s" %
|
||||
SHLIB_EXT],
|
||||
'dirs': []}
|
||||
|
||||
moduleclass = 'numlib'
|
||||
|
||||
@ -12,7 +12,7 @@ toolchain = {'name': 'Py', 'version': '2.7'}
|
||||
source_urls = [PYPI_SOURCE]
|
||||
sources = [SOURCE_TAR_GZ]
|
||||
|
||||
#dependencies = [
|
||||
# dependencies = [
|
||||
# ('six', '1.11.0'),
|
||||
#]
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@ toolchain = {'name': 'Py', 'version': '3.6'}
|
||||
source_urls = [PYPI_SOURCE]
|
||||
sources = [SOURCE_TAR_GZ]
|
||||
|
||||
#dependencies = [
|
||||
# dependencies = [
|
||||
# ('MarkupSafe', '1.0'),
|
||||
#]
|
||||
|
||||
|
||||
@ -8,8 +8,8 @@ versionsuffix = '-Python-2.7.13-base'
|
||||
github_account = 'PyCQA'
|
||||
|
||||
homepage = 'https://github.com/PyCQA/astroid'
|
||||
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
|
||||
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
|
||||
this library is essentially governed by pylint’s needs. It used to be called logilab-astng."""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
@ -21,9 +21,7 @@ dependencies = [
|
||||
('Python', '2.7.13', '-base', True),
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python%(pyshortver)s/site-packages/astroid-%(version)s-py2.7.egg'],
|
||||
}
|
||||
sanity_check_paths = {'files': [], 'dirs': [
|
||||
'lib/python%(pyshortver)s/site-packages/astroid-%(version)s-py2.7.egg'], }
|
||||
|
||||
moduleclass = 'lib'
|
||||
|
||||
@ -16,9 +16,7 @@ dependencies = [
|
||||
('six', '1.11.0'),
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg'],
|
||||
}
|
||||
sanity_check_paths = {'files': [], 'dirs': [
|
||||
'lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg'], }
|
||||
|
||||
moduleclass = 'python'
|
||||
|
||||
@ -16,9 +16,7 @@ dependencies = [
|
||||
('six', '1.11.0'),
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg'],
|
||||
}
|
||||
sanity_check_paths = {'files': [], 'dirs': [
|
||||
'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg'], }
|
||||
|
||||
moduleclass = 'python'
|
||||
|
||||
@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
|
||||
toolchain = {'name': 'foss', 'version': '2015b'}
|
||||
|
||||
source_urls = [SOURCEFORGE_SOURCE]
|
||||
sources = ['%(name)s_%(version)s.tar.gz' ]
|
||||
sources = ['%(name)s_%(version)s.tar.gz']
|
||||
|
||||
java = 'Java'
|
||||
javaver = '1.8.0_66'
|
||||
|
||||
@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
|
||||
toolchain = {'name': 'foss', 'version': '2015b'}
|
||||
|
||||
source_urls = [SOURCEFORGE_SOURCE]
|
||||
sources = ['%(name)s_%(version)s.tar.gz' ]
|
||||
sources = ['%(name)s_%(version)s.tar.gz']
|
||||
|
||||
java = 'Java'
|
||||
javaver = '1.8.0_74'
|
||||
|
||||
@ -10,7 +10,7 @@ description = """BBMap short read aligner, and other bioinformatic tools."""
|
||||
toolchain = {'name': 'intel', 'version': '2016b'}
|
||||
|
||||
source_urls = [SOURCEFORGE_SOURCE]
|
||||
sources = ['%(name)s_%(version)s.tar.gz' ]
|
||||
sources = ['%(name)s_%(version)s.tar.gz']
|
||||
|
||||
dependencies = [('Java', '1.8.0_112', '', True)]
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
|
||||
|
||||
@ -32,7 +33,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2015a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
|
||||
|
||||
@ -32,7 +33,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015g'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
dependencies = [
|
||||
('HTSlib', '1.3'),
|
||||
@ -30,7 +31,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
|
||||
|
||||
@ -34,7 +35,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
source_urls = [
|
||||
'https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
|
||||
patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
|
||||
|
||||
@ -34,7 +35,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -9,25 +9,26 @@ name = 'BCFtools'
|
||||
version = '1.3.1'
|
||||
|
||||
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"""
|
||||
|
||||
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]
|
||||
|
||||
dependencies = [
|
||||
('zlib', '1.2.8'),
|
||||
('GSL', '1.16'),
|
||||
('zlib', '1.2.8'),
|
||||
('GSL', '1.16'),
|
||||
]
|
||||
|
||||
buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'"
|
||||
|
||||
runtest = 'test'
|
||||
|
||||
files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"),
|
||||
"doc", "plugins", "test", "LICENSE", "README", "AUTHORS"]
|
||||
files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"),
|
||||
"doc", "plugins", "test", "LICENSE", "README", "AUTHORS"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/bcftools"],
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
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']
|
||||
|
||||
@ -35,7 +36,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -11,7 +11,8 @@ toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
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']
|
||||
|
||||
@ -35,7 +36,12 @@ postinstallcmds = [
|
||||
]
|
||||
|
||||
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'],
|
||||
}
|
||||
|
||||
|
||||
@ -9,9 +9,9 @@ name = "BEDOPS"
|
||||
version = "2.4.1"
|
||||
|
||||
homepage = 'https://github.com/bedops/bedops'
|
||||
description = """ BEDOPS is an open-source command-line toolkit that performs highly
|
||||
efficient and scalable Boolean and other set operations, statistical calculations,
|
||||
archiving, conversion and other management of genomic data of arbitrary scale."""
|
||||
description = """ BEDOPS is an open-source command-line toolkit that performs highly
|
||||
efficient and scalable Boolean and other set operations, statistical calculations,
|
||||
archiving, conversion and other management of genomic data of arbitrary scale."""
|
||||
|
||||
# this application requires GCC-4.8.x or higher
|
||||
# be aware if you switch to a different toolchain
|
||||
@ -27,9 +27,9 @@ parallel = 1
|
||||
files_to_copy = ["bin"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed",
|
||||
"starchcat", "vcf2bed", "wig2bed",
|
||||
"gtf2bed", "bedops", "wig2bed"]],
|
||||
'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed",
|
||||
"starchcat", "vcf2bed", "wig2bed",
|
||||
"gtf2bed", "bedops", "wig2bed"]],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
|
||||
@ -16,7 +16,8 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
|
||||
|
||||
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']
|
||||
|
||||
sanity_check_paths = {
|
||||
|
||||
@ -22,11 +22,33 @@ dependencies = [('libpng', '1.6.2')]
|
||||
|
||||
buildopts = 'CC="$CC" COPT= L="$LIBS"'
|
||||
|
||||
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
|
||||
files_to_copy = [
|
||||
"bin",
|
||||
"blat",
|
||||
"gfClient",
|
||||
"gfServer",
|
||||
"hg",
|
||||
"inc",
|
||||
"jkOwnLib",
|
||||
"lib",
|
||||
"utils",
|
||||
"webBlat"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
|
||||
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
|
||||
'files': [
|
||||
"bin/%s" %
|
||||
x for x in [
|
||||
'blat',
|
||||
'faToNib',
|
||||
'faToTwoBit',
|
||||
'gfClient',
|
||||
'gfServer',
|
||||
'nibFrag',
|
||||
'pslPretty',
|
||||
'pslReps',
|
||||
'pslSort',
|
||||
'twoBitInfo',
|
||||
'twoBitToFa']],
|
||||
'dirs': files_to_copy,
|
||||
}
|
||||
|
||||
|
||||
@ -26,11 +26,33 @@ dependencies = [(libpng, libpng_ver)]
|
||||
|
||||
buildopts = 'CC="$CC" COPT= L="$LIBS"'
|
||||
|
||||
files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
|
||||
files_to_copy = [
|
||||
"bin",
|
||||
"blat",
|
||||
"gfClient",
|
||||
"gfServer",
|
||||
"hg",
|
||||
"inc",
|
||||
"jkOwnLib",
|
||||
"lib",
|
||||
"utils",
|
||||
"webBlat"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
|
||||
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
|
||||
'files': [
|
||||
"bin/%s" %
|
||||
x for x in [
|
||||
'blat',
|
||||
'faToNib',
|
||||
'faToTwoBit',
|
||||
'gfClient',
|
||||
'gfServer',
|
||||
'nibFrag',
|
||||
'pslPretty',
|
||||
'pslReps',
|
||||
'pslSort',
|
||||
'twoBitInfo',
|
||||
'twoBitToFa']],
|
||||
'dirs': files_to_copy,
|
||||
}
|
||||
|
||||
|
||||
@ -22,11 +22,33 @@ dependencies = [('libpng', '1.6.6')]
|
||||
|
||||
buildopts = 'CC="$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 = {
|
||||
'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
|
||||
'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
|
||||
'files': [
|
||||
"bin/%s" %
|
||||
x for x in [
|
||||
'blat',
|
||||
'faToNib',
|
||||
'faToTwoBit',
|
||||
'gfClient',
|
||||
'gfServer',
|
||||
'nibFrag',
|
||||
'pslPretty',
|
||||
'pslReps',
|
||||
'pslSort',
|
||||
'twoBitInfo',
|
||||
'twoBitToFa']],
|
||||
'dirs': files_to_copy,
|
||||
}
|
||||
|
||||
|
||||
@ -4,16 +4,17 @@ name = 'BLCR'
|
||||
version = '0.8.5'
|
||||
|
||||
homepage = 'http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/'
|
||||
description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers
|
||||
are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide
|
||||
a robust, production quality implementation that checkpoints a wide range of applications,
|
||||
description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers
|
||||
are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide
|
||||
a robust, production quality implementation that checkpoints a wide range of applications,
|
||||
without requiring changes to be made to application code. """
|
||||
|
||||
toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
source_urls = [('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')]
|
||||
source_urls = [
|
||||
('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['include/libcr.h'],
|
||||
|
||||
@ -12,7 +12,7 @@ source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
|
||||
dependencies = [
|
||||
('zlib', '1.2.11', '', True),
|
||||
('zlib', '1.2.11', '', True),
|
||||
]
|
||||
|
||||
moduleclass = 'bio'
|
||||
|
||||
@ -8,10 +8,10 @@ name = 'BXH_XCEDE_TOOLS'
|
||||
version = '1.11.1'
|
||||
|
||||
homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/'
|
||||
description = """A collection of data processing and image analysis
|
||||
tools for data in BXH or XCEDE format. This includes data format
|
||||
encapsulation/conversion, event-related analysis, QA tools, and more.
|
||||
These tools form the basis of the fBIRN QA procedures and are also
|
||||
description = """A collection of data processing and image analysis
|
||||
tools for data in BXH or XCEDE format. This includes data format
|
||||
encapsulation/conversion, event-related analysis, QA tools, and more.
|
||||
These tools form the basis of the fBIRN QA procedures and are also
|
||||
distributed as part of the fBIRN Data Upload Scripts."""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': 'dummy'}
|
||||
@ -25,4 +25,3 @@ sanity_check_paths = {
|
||||
}
|
||||
|
||||
moduleclass = 'bio'
|
||||
|
||||
|
||||
@ -16,8 +16,8 @@ name = 'Bash'
|
||||
version = '4.2'
|
||||
|
||||
homepage = 'http://www.gnu.org/software/bash'
|
||||
description = """Bash is an sh-compatible command language interpreter that executes commands
|
||||
read from the standard input or from a file. Bash also incorporates useful features from the
|
||||
description = """Bash is an sh-compatible command language interpreter that executes commands
|
||||
read from the standard input or from a file. Bash also incorporates useful features from the
|
||||
Korn and C shells (ksh and csh)."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2015b'}
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -9,9 +9,9 @@ name = 'BayPass'
|
||||
version = '2.1'
|
||||
|
||||
homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html'
|
||||
description = """BayPass is a population genomics software which is primarily aimed at identifying
|
||||
genetic markers subjected to selection and/or associated to population-specific covariates
|
||||
(e.g., environmental variables, quantitative or categorical phenotypic characteristics).
|
||||
description = """BayPass is a population genomics software which is primarily aimed at identifying
|
||||
genetic markers subjected to selection and/or associated to population-specific covariates
|
||||
(e.g., environmental variables, quantitative or categorical phenotypic characteristics).
|
||||
The underlying models explicitly account for (and may estimate) the covariance structure among the
|
||||
population allele frequencies that originates from the shared history of the populations under study"""
|
||||
|
||||
@ -25,12 +25,12 @@ start_dir = 'sources'
|
||||
|
||||
parallel = 1
|
||||
|
||||
files_to_copy = [(['sources/g_baypass'], 'bin/'),
|
||||
'BayPass_manual_2.1.pdf',
|
||||
'examples',
|
||||
'Licence_CeCILL-B_V1-en.txt',
|
||||
'utils'
|
||||
]
|
||||
files_to_copy = [(['sources/g_baypass'], 'bin/'),
|
||||
'BayPass_manual_2.1.pdf',
|
||||
'examples',
|
||||
'Licence_CeCILL-B_V1-en.txt',
|
||||
'utils'
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/g_baypass'],
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -20,10 +20,11 @@ sources = ['v%(version)s.tar.gz']
|
||||
|
||||
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
|
||||
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bayescenv'],
|
||||
'dirs': [],
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -19,10 +19,11 @@ sources = ['v%(version)s.tar.gz']
|
||||
|
||||
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
|
||||
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bayescenv'],
|
||||
'dirs': [],
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -9,7 +9,7 @@ name = 'BayeScan'
|
||||
version = '2.1'
|
||||
|
||||
homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
|
||||
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
|
||||
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
|
||||
using differences in allele frequencies between populations."""
|
||||
|
||||
toolchain = {'name': 'foss', 'version': '2016a'}
|
||||
@ -30,7 +30,7 @@ files_to_copy = [
|
||||
]
|
||||
|
||||
parallel = 1
|
||||
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bayescan_%(version)s'],
|
||||
'dirs': [],
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# sciCORE - University of Basel
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
# SIB Swiss Institute of Bioinformatics
|
||||
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
@ -9,10 +9,11 @@ name = 'BayeScan'
|
||||
version = '2.1'
|
||||
|
||||
homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
|
||||
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
|
||||
description = """BayeScan aims at identifying candidate loci under natural selection from genetic data,
|
||||
using differences in allele frequencies between populations."""
|
||||
|
||||
# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile
|
||||
# BayeScan makefile is hardcoded to use g++. In case you want to use a
|
||||
# non-gcc toolchain you will need to patch the makefile
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
toolchainopts = {'openmp': True}
|
||||
|
||||
@ -31,7 +32,7 @@ files_to_copy = [
|
||||
'R functions']
|
||||
|
||||
parallel = 1
|
||||
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bayescan_%(version)s'],
|
||||
'dirs': [],
|
||||
|
||||
@ -4,24 +4,25 @@ name = 'BayesAss'
|
||||
version = '3.0.4'
|
||||
|
||||
homepage = 'http://www.rannala.org/?page_id=245'
|
||||
description = """
|
||||
BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
|
||||
description = """
|
||||
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']
|
||||
|
||||
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 = [
|
||||
('GSL','2.1')
|
||||
('GSL', '2.1')
|
||||
]
|
||||
|
||||
runtest = 'check'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/BA3'],
|
||||
'dirs' : ['bin', 'include']
|
||||
'dirs': ['bin', 'include']
|
||||
}
|
||||
|
||||
moduleclass = 'bio'
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
|
||||
easyblock = "CmdCp"
|
||||
|
||||
@ -6,7 +6,7 @@ name = 'Bazel'
|
||||
version = '0.3.0'
|
||||
|
||||
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."""
|
||||
|
||||
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')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': ['bin'],
|
||||
}
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# @author: Robert Schmidt (OHRI)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
|
||||
easyblock = "CmdCp"
|
||||
|
||||
@ -7,13 +7,14 @@ name = 'Bazel'
|
||||
version = '0.4.4'
|
||||
|
||||
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."""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': 'dummy'}
|
||||
|
||||
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 = [
|
||||
('Java', '1.8.0_121'),
|
||||
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
|
||||
|
||||
files_to_copy = [(['output/bazel'], 'bin')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': [],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# @author: Robert Schmidt (OHRI)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
|
||||
easyblock = "CmdCp"
|
||||
|
||||
@ -7,13 +7,14 @@ name = 'Bazel'
|
||||
version = '0.5.0'
|
||||
|
||||
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."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '4.9.3-tf'}
|
||||
|
||||
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 = [
|
||||
('Java', '1.8.0_121', '', True),
|
||||
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
|
||||
|
||||
files_to_copy = [(['output/bazel'], 'bin')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': [],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# @author: Robert Schmidt (OHRI)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
|
||||
easyblock = "CmdCp"
|
||||
|
||||
@ -7,13 +7,14 @@ name = 'Bazel'
|
||||
version = '0.5.0'
|
||||
|
||||
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."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
|
||||
|
||||
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 = [
|
||||
('Java', '1.8.0_121', '', True),
|
||||
@ -23,9 +24,9 @@ cmds_map = [('.*', "./compile.sh")]
|
||||
|
||||
files_to_copy = [(['output/bazel'], 'bin')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': [],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
# @author: Robert Schmidt (OHRI)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
# @author: Guilherme Peretti-Pezzi (CSCS)
|
||||
|
||||
easyblock = "CmdCp"
|
||||
|
||||
@ -7,13 +7,14 @@ name = 'Bazel'
|
||||
version = '0.5.1'
|
||||
|
||||
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."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
|
||||
|
||||
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 = [
|
||||
('cc_configure.patch'),
|
||||
@ -30,9 +31,9 @@ cmds_map = [('.*', "./compile.sh")]
|
||||
|
||||
files_to_copy = [(['output/bazel'], 'bin')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': [],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -13,7 +13,8 @@ It is used to build the majority of Google's software."""
|
||||
toolchain = {'name': 'GCC', 'version': '7.1.0-2.28'}
|
||||
|
||||
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 = [
|
||||
('cc_configure.patch'),
|
||||
@ -30,9 +31,9 @@ cmds_map = [('.*', "./compile.sh")]
|
||||
|
||||
files_to_copy = [(['output/bazel'], 'bin')]
|
||||
|
||||
sanity_check_paths={
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/bazel'],
|
||||
'dirs': [],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -7,7 +7,8 @@ It is used to build the majority of Google's software."""
|
||||
|
||||
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']
|
||||
checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416']
|
||||
|
||||
|
||||
@ -7,7 +7,8 @@ It is used to build the majority of Google's software."""
|
||||
|
||||
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']
|
||||
checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416']
|
||||
|
||||
|
||||
@ -9,16 +9,17 @@ name = 'Beast'
|
||||
version = '1.8.4'
|
||||
|
||||
homepage = 'http://beast.bio.ed.ac.uk/'
|
||||
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
|
||||
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
|
||||
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
|
||||
but is also a framework for testing evolutionary hypotheses without conditioning on a single
|
||||
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
|
||||
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
|
||||
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using
|
||||
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies
|
||||
but is also a framework for testing evolutionary hypotheses without conditioning on a single
|
||||
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted
|
||||
proportional to its posterior probability. """
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
|
||||
source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/']
|
||||
source_urls = [
|
||||
'https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/']
|
||||
sources = ['BEASTv%(version)s.tgz']
|
||||
|
||||
dependencies = [
|
||||
|
||||
@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
|
||||
installopts = 'INSTDIR=%(installdir)s'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/'+prog+'.'+flavor+'.x'
|
||||
'files': ['bin/' + prog + '.' + flavor + '.x'
|
||||
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
|
||||
for flavor in ['real', 'cplx']],
|
||||
'dirs': []
|
||||
|
||||
@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
|
||||
installopts = 'INSTDIR=%(installdir)s'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/'+prog+'.'+flavor+'.x'
|
||||
'files': ['bin/' + prog + '.' + flavor + '.x'
|
||||
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
|
||||
for flavor in ['real', 'cplx']],
|
||||
'dirs': []
|
||||
|
||||
@ -4,9 +4,9 @@ name = 'BerkeleyUPC'
|
||||
version = '2.16.2'
|
||||
|
||||
homepage = 'http://upc.lbl.gov'
|
||||
description = """The goal of the Berkeley UPC compiler group is to develop a portable,
|
||||
high performance implementation of UPC for large-scale multiprocessors, PC clusters,
|
||||
and clusters of shared memory multiprocessors.
|
||||
description = """The goal of the Berkeley UPC compiler group is to develop a portable,
|
||||
high performance implementation of UPC for large-scale multiprocessors, PC clusters,
|
||||
and clusters of shared memory multiprocessors.
|
||||
"""
|
||||
|
||||
toolchain = {'name': 'gompi', 'version': '2015b'}
|
||||
@ -19,7 +19,7 @@ sources = ['berkeley_upc-%(version)s.tar.gz']
|
||||
preconfigopts = './Bootstrap -L && '
|
||||
preconfigopts += 'export CFLAGS="$OPTFLAGS -fopenmp -Wl,-rpath,$EBROOTGCC/lib64" && '
|
||||
# Manually create build directory
|
||||
preconfigopts += 'mkdir build && cd build && '
|
||||
preconfigopts += 'mkdir build && cd build && '
|
||||
|
||||
# To be able run "../configure"
|
||||
configure_cmd_prefix = "."
|
||||
|
||||
@ -27,8 +27,8 @@ exts_list = [
|
||||
}),
|
||||
(name, version, {
|
||||
'modulename': 'Bio::Perl',
|
||||
'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'),
|
||||
'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'],
|
||||
'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'),
|
||||
'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'],
|
||||
}),
|
||||
]
|
||||
|
||||
@ -37,4 +37,3 @@ modextrapaths = {
|
||||
}
|
||||
|
||||
moduleclass = 'bio'
|
||||
|
||||
|
||||
@ -34,11 +34,11 @@ dependencies = [
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
|
||||
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver),
|
||||
'lib/python%s/site-packages/BioSQL' % pyshortver]
|
||||
}
|
||||
'files': [], 'dirs': [
|
||||
'lib/python%s/site-packages/Bio' %
|
||||
pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' %
|
||||
(pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' %
|
||||
pyshortver]}
|
||||
|
||||
options = {'modulename': 'Bio'}
|
||||
|
||||
|
||||
@ -34,11 +34,11 @@ dependencies = [
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
|
||||
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version, pyshortver),
|
||||
'lib/python%s/site-packages/BioSQL' % pyshortver]
|
||||
}
|
||||
'files': [], 'dirs': [
|
||||
'lib/python%s/site-packages/Bio' %
|
||||
pyshortver, 'lib/python%s/site-packages/biopython-%s-py%s.egg-info' %
|
||||
(pyshortver, version, pyshortver), 'lib/python%s/site-packages/BioSQL' %
|
||||
pyshortver]}
|
||||
|
||||
options = {'modulename': 'Bio'}
|
||||
|
||||
|
||||
@ -29,8 +29,9 @@ dependencies = [
|
||||
|
||||
sanity_check_paths = {
|
||||
'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'}
|
||||
|
||||
|
||||
@ -33,8 +33,9 @@ dependencies = [
|
||||
|
||||
sanity_check_paths = {
|
||||
'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'}
|
||||
|
||||
|
||||
@ -29,8 +29,9 @@ dependencies = [
|
||||
|
||||
sanity_check_paths = {
|
||||
'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'}
|
||||
|
||||
|
||||
@ -29,8 +29,9 @@ dependencies = [
|
||||
|
||||
sanity_check_paths = {
|
||||
'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'}
|
||||
|
||||
|
||||
@ -28,9 +28,7 @@ builddependencies = [
|
||||
|
||||
options = {'modulename': 'BoltzTraP2'}
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'],
|
||||
}
|
||||
sanity_check_paths = {'files': [], 'dirs': [
|
||||
'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'], }
|
||||
|
||||
moduleclass = 'python'
|
||||
|
||||
@ -28,9 +28,7 @@ builddependencies = [
|
||||
|
||||
options = {'modulename': 'BoltzTraP2'}
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': [],
|
||||
'dirs': ['lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'],
|
||||
}
|
||||
sanity_check_paths = {'files': [], 'dirs': [
|
||||
'lib/python3.6/site-packages/%(name)s-%(version)s-py3.6-linux-x86_64.egg/%(name)s'], }
|
||||
|
||||
moduleclass = 'python'
|
||||
|
||||
@ -21,6 +21,6 @@ dependencies = [
|
||||
# also build boost_mpi
|
||||
boost_mpi = True
|
||||
|
||||
osdependencies = [('zlib-devel','zlib1g-dev')]
|
||||
osdependencies = [('zlib-devel', 'zlib1g-dev')]
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -4,7 +4,7 @@ version = '1.58.0'
|
||||
homepage = 'http://www.boost.org/'
|
||||
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}
|
||||
|
||||
source_urls = [SOURCEFORGE_SOURCE]
|
||||
|
||||
@ -18,13 +18,13 @@ pythonversion = '2.7.11'
|
||||
versionsuffix = '-Python-%s' % pythonversion
|
||||
|
||||
dependencies = [
|
||||
('bzip2', '1.0.6' ),
|
||||
('bzip2', '1.0.6'),
|
||||
('Python', pythonversion),
|
||||
]
|
||||
|
||||
# also build boost_mpi
|
||||
boost_mpi = True
|
||||
|
||||
osdependencies = [('zlib-devel','zlib1g-dev')]
|
||||
osdependencies = [('zlib-devel', 'zlib1g-dev')]
|
||||
|
||||
moduleclass = 'devel'
|
||||
|
||||
@ -9,16 +9,18 @@ name = 'Bowtie2'
|
||||
version = '2.0.5'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),
|
||||
|
||||
@ -9,16 +9,18 @@ name = 'Bowtie2'
|
||||
version = '2.0.6'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),
|
||||
|
||||
@ -9,16 +9,18 @@ name = 'Bowtie2'
|
||||
version = '2.1.0'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'),
|
||||
|
||||
@ -9,24 +9,38 @@ name = 'Bowtie2'
|
||||
version = '2.2.0'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
|
||||
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
|
||||
"doc", "example", "scripts"]
|
||||
files_to_copy = [(["bowtie2",
|
||||
"bowtie2-align-l",
|
||||
"bowtie2-align-s",
|
||||
"bowtie2-build",
|
||||
"bowtie2-build-l",
|
||||
"bowtie2-build-s",
|
||||
"bowtie2-inspect",
|
||||
"bowtie2-inspect-l",
|
||||
"bowtie2-inspect-s"],
|
||||
'bin'),
|
||||
"doc",
|
||||
"example",
|
||||
"scripts"]
|
||||
|
||||
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': [],
|
||||
}
|
||||
|
||||
|
||||
@ -9,24 +9,41 @@ name = 'Bowtie2'
|
||||
version = '2.2.2'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
|
||||
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
|
||||
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"]
|
||||
files_to_copy = [(["bowtie2",
|
||||
"bowtie2-align-l",
|
||||
"bowtie2-align-s",
|
||||
"bowtie2-build",
|
||||
"bowtie2-build-l",
|
||||
"bowtie2-build-s",
|
||||
"bowtie2-inspect",
|
||||
"bowtie2-inspect-l",
|
||||
"bowtie2-inspect-s"],
|
||||
'bin'),
|
||||
"doc",
|
||||
"example",
|
||||
"scripts",
|
||||
"MANUAL",
|
||||
"MANUAL.markdown",
|
||||
"NEWS"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"],
|
||||
'files': [
|
||||
"bin/bowtie2-align-l",
|
||||
"bin/bowtie2-build",
|
||||
"bin/bowtie2-inspect"],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
|
||||
@ -11,24 +11,41 @@ name = 'Bowtie2'
|
||||
version = '2.2.4'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.4.10'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
|
||||
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
|
||||
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"]
|
||||
files_to_copy = [(["bowtie2",
|
||||
"bowtie2-align-l",
|
||||
"bowtie2-align-s",
|
||||
"bowtie2-build",
|
||||
"bowtie2-build-l",
|
||||
"bowtie2-build-s",
|
||||
"bowtie2-inspect",
|
||||
"bowtie2-inspect-l",
|
||||
"bowtie2-inspect-s"],
|
||||
'bin'),
|
||||
"doc",
|
||||
"example",
|
||||
"scripts",
|
||||
"MANUAL",
|
||||
"MANUAL.markdown",
|
||||
"NEWS"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"],
|
||||
'files': [
|
||||
"bin/bowtie2-align-l",
|
||||
"bin/bowtie2-build",
|
||||
"bin/bowtie2-inspect"],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
|
||||
@ -11,24 +11,41 @@ name = 'Bowtie2'
|
||||
version = '2.2.5'
|
||||
|
||||
homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
|
||||
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
|
||||
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
|
||||
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
|
||||
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
|
||||
|
||||
toolchain = {'name': 'goolf', 'version': '1.7.20'}
|
||||
|
||||
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 = [
|
||||
(["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
|
||||
"bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
|
||||
"doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"]
|
||||
files_to_copy = [(["bowtie2",
|
||||
"bowtie2-align-l",
|
||||
"bowtie2-align-s",
|
||||
"bowtie2-build",
|
||||
"bowtie2-build-l",
|
||||
"bowtie2-build-s",
|
||||
"bowtie2-inspect",
|
||||
"bowtie2-inspect-l",
|
||||
"bowtie2-inspect-s"],
|
||||
'bin'),
|
||||
"doc",
|
||||
"example",
|
||||
"scripts",
|
||||
"MANUAL",
|
||||
"MANUAL.markdown",
|
||||
"NEWS"]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"],
|
||||
'files': [
|
||||
"bin/bowtie2-align-l",
|
||||
"bin/bowtie2-build",
|
||||
"bin/bowtie2-inspect"],
|
||||
'dirs': [],
|
||||
}
|
||||
|
||||
|
||||
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Reference in New Issue
Block a user