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add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 #17140

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Jan 20, 2023
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add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 #17140

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30 changes: 10 additions & 20 deletions easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb
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Expand Up @@ -15,11 +15,13 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ
patches = [
'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch',
'ncbi-vdb-cstdlib.patch',
'ncbi-vdb-3.0.0_hdf5_api.patch',
]
checksums = [
'154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7', # ncbi-vdb-3.0.0.tar.gz
'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch
'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch
{'ncbi-vdb-3.0.0.tar.gz': '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7'},
{'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch': 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133'},
{'ncbi-vdb-cstdlib.patch': 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655'},
{'ncbi-vdb-3.0.0_hdf5_api.patch': '34bdad822248118a011b5106fe5b5efaa068c19b66ed10f949a9c0b07a79de8b'},
]

builddependencies = [
Expand All @@ -29,29 +31,17 @@ builddependencies = [
]

dependencies = [
('file', '5.43'), # provides libmagic
('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible
('HDF5', '1.12.2'),
('libxml2', '2.9.13'),
('bzip2', '1.0.8'),
]

# add addtional libraries needed to statically link HDF5 from EB
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preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/'"
preconfigopts += " %(builddir)s/%(namelower)s-%(version)s/setup/konfigure.perl &&"

configopts = ''
configopts += ' -DHDF5_LIBDIR=$EBROOTHDF5/lib -DXML2_LIBDIR=$EBROOTLIBXML2/lib'
configopts += ' -DHDF5_INCDIR=$EBROOTHDF5/include -DXML2_INCDIR=$EBROOTLIBXML2/include'


# replace hardcoded optimization flags with EB settings
prebuildopts = "find %(builddir)s/%(namelower)s-%(version)s/build/ -name \"Makefile*\" "
prebuildopts += "-exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" "
preinstallopts = 'EBFLAGS="$CFLAGS" '
configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib "
configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib "

sanity_check_paths = {
'files': [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e))
for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]],
'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] +
[('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]],
'dirs': [],
}

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4 changes: 2 additions & 2 deletions test/easyconfigs/easyconfigs.py
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Expand Up @@ -504,9 +504,9 @@ def check_dep_vars(self, gen, dep, dep_vars):
r'QGIS-3\.28\.1']),
],
'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])],
# ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb)
# ncbi-vdb v2.x requires HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb)
'HDF5': [
(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.',
(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.',
r'shovill-1\.1\.']),
],
# VMTK 1.4.x requires ITK 4.13.x
Expand Down