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#435 PR version
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pavelToman committed Oct 17, 2024
1 parent 531f4e9 commit 2d7cee1
Showing 1 changed file with 0 additions and 63 deletions.
63 changes: 0 additions & 63 deletions 435_cisDiversity/cisDiv.eb
Original file line number Diff line number Diff line change
Expand Up @@ -16,64 +16,11 @@ sources = [{
}]
checksums = ['4ba5967fa754ec78b9dd6b6dc9d2ee5de87dbb4d7906d47e57e73aec87897725']

# builddependencies = [('patchelf', '0.18.0')]
dependencies = [
('Python', '2.7.18'),
('SciPy-bundle', '2020.03', '-Python-%(pyver)s'),
('R', '3.6.3'),
]

# exts_defaultclass = 'PythonPackage'
# exts_default_options = {
# 'source_urls': [PYPI_SOURCE],
# 'download_dep_fail': True,
# 'use_pip': True,
# 'sanity_pip_check': True,
# 'preinstallopts': '',
# 'installopts': '',
# }

# exts_list = [
# ('Paralleltask', '0.2.3', {
# 'modulename': 'paralleltask',
# 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'],
# }),
# ]

# # fix make -C util - warning: jobserver unavailable
# parallel = 1

# # fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83
# # + use SAMtools and minimap2 from EB
# prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count/' Makefile && "
# prebuildopts += "rm -rf util/bwa && rm -fr util/minimap2 && rm -rf util/samtools && "
# prebuildopts += (
# "sed -i"
# " -e 's/seq_split seq_count bwa_ samtools_ minimap2_/seq_split seq_count/'"
# " -e '/BWADIR/d'"
# " -e '/bwa_:/d'"
# " -e '/SAMTOOLSDIR/d'"
# " -e '/MINIMAP2DIR/d'"
# " -e '/samtools_:/d'"
# " -e '/minimap2_:/d'"
# " util/Makefile && "
# )
# postinstallcmds = [
# # links to binaries
# "cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa && "
# "ln -s $EBROOTSAMTOOLS/bin/samtools && ln -s $EBROOTMINIMAP2/bin/minimap2",
# # set RPATH to calgs.so, nextpolish1.so and nextpolish2.so
# "if %(rpath_enabled)s; then "
# "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
# '":$EBROOTZLIB/lib" %(installdir)s/lib/calgs.so && '
# "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
# '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish1.so && '
# "patchelf --force-rpath --set-rpath '$ORIGIN:$ORIGIN/../lib'"
# '"$EBROOTZLIB/lib:$EBROOTBZIP2/lib:$EBROOTXZ/lib" %(installdir)s/lib/nextpolish2.so; fi',
# ]

# files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish']
# files_to_copy = ['*']
files_to_copy = [(['learnDiverseModules'], 'bin')]

sanity_check_paths = {
Expand All @@ -83,14 +30,4 @@ sanity_check_paths = {

sanity_check_commands = ['learnDiverseModules -h']

# modextrapaths = {
# 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
# 'PATH': '',
# }

moduleclass = 'bio'

# builddir:
# /tmp/vsc47063/easybuild/build/cisDIVERSITY/1.1/foss-2020a
# installdir:
# scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cisDIVERSITY/1.1-foss-2020a

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