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adding easyconfigs: VEP-113.3-GCC-13.3.0.eb
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name = 'VEP' | ||
version = '113.3' | ||
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homepage = 'https://www.ensembl.org/info/docs/tools/vep' | ||
description = """Variant Effect Predictor (VEP) determines the effect of your | ||
variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, | ||
transcripts, and protein sequence, as well as regulatory regions. | ||
Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently | ||
used routines in VEP.""" | ||
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toolchain = {'name': 'GCC', 'version': '13.3.0'} | ||
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source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] | ||
sources = ['%(version)s.tar.gz'] | ||
checksums = ['ee68013eb035e17129e8f69977f525ebdd8321e73b3164a7bda6e103e2d10beb'] | ||
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dependencies = [ | ||
('Perl', '5.38.2'), | ||
('Archive-Zip', '1.68'), | ||
('DBD-mysql', '4.051'), | ||
('BioPerl', '1.7.8'), | ||
('Bio-DB-HTS', '3.01'), | ||
# VEP requires Compress::Raw::Zlib >= 2.103 | ||
('Compress-Raw-Zlib', '2.213'), | ||
] | ||
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# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed | ||
# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) | ||
species = 'cyprinus_carpio_carpio' | ||
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exts_defaultclass = 'PerlModule' | ||
exts_filter = ("perl -e 'require %(ext_name)s'", "") | ||
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exts_list = [ | ||
('Bio::EnsEMBL::XS', '2.3.2', { | ||
'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], | ||
'sources': ['%(version)s.tar.gz'], | ||
'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], | ||
}), | ||
] | ||
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sanity_check_commands = ['vep --help'] | ||
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moduleclass = 'bio' |