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BCFtools-1.15.1-cpeGNU-22.06.eb
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BCFtools-1.15.1-cpeGNU-22.06.eb
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# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Author: Jonas Demeulemeester
# The Francis Crick Insitute, London, UK
easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.15.1'
homepage = 'https://www.htslib.org/'
whatis = [
"Description: BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants",
]
description = """i
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (
VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs,
both uncompressed and BGZF-compressed.
It used to be part of SAMtools, a suite of programs for interacting with high-throughput
sequencing data.
This version is compiled using GSL without OpenMP support, so no parallel BLAS etc.
"""
toolchain = {'name': 'cpeGNU', 'version': '22.06'}
toolchainopts = {'pic': True}
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
sources = [SOURCELOWER_TAR_BZ2]
checksums = ['f21f9564873eb27ccf22d13b91a64acb8fbbfe4f9e4c37933a54b9a95857f2d7']
builddependencies = [
('buildtools', '%(toolchain_version)s', '', True),
]
dependencies = [
# ('zlib', '1.2.12'),
# ('libdeflate', '1.12'),
# ('bzip2', '1.0.8'),
# ('XZ', '5.2.5'),
('GSL', '2.7.1', '-sequential'),
('HTSlib', '1.15.1'),
]
# As linking with BLAS is automatic on Cray systems, the configure script goes wrong and
# then tries to generate some invalid arguments to link/. As a workaround, we tell to
# use libm as the cblas library. It will add -lm twice to the link line but that does no
# harm.
configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl --with-cblas=m "
sanity_check_paths = {
'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
'dirs': ['libexec/bcftools']
}
sanity_check_commands = [
'bcftools -v',
'bcftools plugin -lv',
]
# Needed to use BCFtools plugins
modextravars = {'BCFTOOLS_PLUGINS': '%(installdir)s/libexec/bcftools'}
moduleclass = 'bio'