SAMtools/1.14-cpeGNU-21.12 (SAMtools-1.14-cpeGNU-21.12.eb)
This software is archived in the LUMI-EasyBuild-contrib GitHub repository as easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-1.14-cpeGNU-21.12.eb. The corresponding module would be SAMtools/1.14-cpeGNU-21.12.
##
# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
# Homepage: https://staff.flinders.edu.au/research/deep-thought
#
# Authors:: Robert Qiao <rob.qiao@flinders.edu.au>
# License:: MIT
#
# Notes::
#
# Updated to 1.14 and gcc-11.2.0
# J. Sassmannshausen / GSTT
easyblock = 'EB_SAMtools'
name = 'SAMtools'
version = '1.14'
homepage = 'https://www.htslib.org/'
whatis = [
"Description: SAMtools is a collection of utilities for the Sequence Alignment/Map (SAM) format",
"The module provides a static library (libbam.a) and a number of executables and scripts",
]
description = """
SAMtools provide various utilities for manipulating alignments in the SAM
format, including sorting, merging, indexing and generating alignments in a
per-position format.
SAMtools is implemented as a couple of executables and a number of scripts.
Some scripts (in particular the LUA scripts) may require additional modules.
"""
docurls = [
"Manual page for the samtools and wgsim commands (section 1)",
]
toolchain = {'name': 'cpeGNU', 'version': '21.12'}
toolchainopts = {'pic': True}
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
sources = [SOURCELOWER_TAR_BZ2]
checksums = ['9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74']
builddependencies = [
('buildtools', '%(toolchain_version)s', '', True),
]
# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression.
# The latter is currently provided by XZ.
dependencies = [
('ncurses', '6.2'),
('zlib', '1.2.11'),
('bzip2', '1.0.8'),
('XZ', '5.2.5'),
('cURL', '7.78.0'),
('HTSlib', '1.14'),
]
configopts = '--with-htslib=$EBROOTHTSLIB'
sanity_check_commands = [
'samtools version'
]
moduleclass = 'bio'