diff --git a/435_cisDiversity/cisDiv.eb b/435_cisDiversity/cisDiv.eb index f929ff6..268782e 100644 --- a/435_cisDiversity/cisDiv.eb +++ b/435_cisDiversity/cisDiv.eb @@ -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 = { @@ -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 \ No newline at end of file