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{bio}[foss/2019a] VEP v96.0 #8733

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43 changes: 43 additions & 0 deletions easybuild/easyconfigs/v/VEP/VEP-96.0-foss-2019a-Perl-5.28.1.eb
Original file line number Diff line number Diff line change
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name = 'VEP'
version = '96.0'
versionsuffix = '-Perl-%(perlver)s'

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."""

toolchain = {'name': 'foss', 'version': '2019a'}

source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/']
sources = ['%(version)s.tar.gz']
checksums = ['338f4774683da45e53bdf9a2cfffad4803df53fc4d3ee72817a9e79e63e513f7']

dependencies = [
('Perl', '5.28.1'),
('DBD-mysql', '4.050', versionsuffix),
('BioPerl', '1.7.2', versionsuffix),
('Bio-DB-HTS', '3.01', versionsuffix),
]

exts_defaultclass = 'PerlModule'
exts_filter = ("perldoc -lm %(ext_name)s ", "")

exts_list = [
('Bio::EnsEMBL::XS', '2.3.2', {
'source_tmpl': '%(version)s.tar.gz',
'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'],
'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'],
}),
]

# Add sanity check of EnsEMBL-XS, vep easyblock already takes care of VEP
sanity_check_paths = {
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'files': [],
'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/EnsEMBL/XS'],
}

# Add path for EnsEMBL-XS, vep easyblock takes care of paths for VEP
modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'}

moduleclass = 'bio'