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use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 #18236

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Merged
branfosj merged 3 commits into from
Jun 29, 2023
Merged

use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 #18236

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b11c428
use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2
boegel Jun 29, 2023
b5427ea
remove exception for HDF5 1.10.x dependency variant via ncbi-vdb 2.11…
boegel Jun 29, 2023
6f3fe40
add checksum for ncbi-vdb-3.0.0_hdf5_api.patch in easyconfig for ncbi…
boegel Jun 29, 2023
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10 changes: 6 additions & 4 deletions easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb
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Original file line number Diff line number Diff line change
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 = [
'647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf', # ncbi-vdb-2.11.2.tar.gz
'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch
'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch
{'ncbi-vdb-2.11.2.tar.gz': '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf'},
{'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 @@ -31,7 +33,7 @@ builddependencies = [
dependencies = [
('NGS', '2.11.2'),
('file', '5.41'), # provides libmagic
('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible
('HDF5', '1.12.1'),
('libxml2', '2.9.10'),
('bzip2', '1.0.8'),
]
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5 changes: 0 additions & 5 deletions test/easyconfigs/easyconfigs.py
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Expand Up @@ -509,11 +509,6 @@ 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 requires HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb)
'HDF5': [
(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
'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])],
# Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x)
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