BCFtools/1.18-cpeGNU-23.09 (BCFtools-1.18-cpeGNU-23.09.eb)
Install with the EasyBuild-user module:
To access module help after installation and get reminded for which stacks and partitions the module is installed, usemodule spider BCFtools/1.18-cpeGNU-23.09
.
EasyConfig:
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Author: Jonas Demeulemeester
# The Francis Crick Insitute, London, UK
easyblock = 'ConfigureMake'
local_BCFtools_version = '1.18' # https://github.com/samtools/bcftools/releases
# Dependencies from the main software stack
local_GSL_version = '2.7.1' # https://ftp.gnu.org/gnu/gsl/
# Dependencies from the contributed applications
local_HTSlib_version = '1.18' # https://github.com/samtools/htslib/releases
name = 'BCFtools'
version = local_BCFtools_version
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': '23.09'}
toolchainopts = {'pic': True}
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
sources = [SOURCELOWER_TAR_BZ2]
checksums = ['d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e']
builddependencies = [
('buildtools', '%(toolchain_version)s', '', True),
]
dependencies = [
# ('zlib', '1.2.12'),
# ('libdeflate', '1.12'),
# ('bzip2', '1.0.8'),
# ('XZ', '5.2.5'),
('GSL', local_GSL_version, '-sequential'),
('HTSlib', local_HTSlib_version),
]
# 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 "
postinstallcmds = [
'mkdir -p %(installdir)s/share/licenses/%(name)s ; cp LICENSE AUTHORS NEWS README %(installdir)s/share/licenses/%(name)s'
]
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'