[SAMtools] [package list]

SAMtools/1.24-cpeGNU-26.03 (SAMtools-1.24-cpeGNU-26.03.eb)

Install with the EasyBuild-user module:

eb SAMtools-1.24-cpeGNU-26.03.eb -r

To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider SAMtools/1.24-cpeGNU-26.03.

EasyConfig:

##
# 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
# K. Lust: Updated to 1.15.1.
easyblock = 'EB_SAMtools'

local_SAMtools_version =     '1.24'          # https://github.com/samtools/samtools/releases

# Dependencies from the main software stack
local_ncurses_version =      '6.6'           # https://ftp.gnu.org/pub/gnu/ncurses/

# Dependencies from the contributed applications
local_HTSlib_version =       '1.24'          # https://github.com/samtools/htslib/releases

name =    'SAMtools'
version = local_SAMtools_version

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.
"""

doc_urls = [
    "Manual page for the samtools and wgsim commands (section 1)",
]

toolchain = {'name': 'cpeGNU', 'version': '26.03'}
toolchain_opts = {'pic': True}

source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
sources =     [SOURCELOWER_TAR_BZ2]
checksums =   ['89b2a440123eeaa400392ce1736e7d60ce9041843027d76819753c5a8246bfdd']

build_deps = [
    ('buildtools',          '%(toolchain_version)s', '', True),
    ('craype-accel-none',   EXTERNAL_MODULE),
    ('craype-network-none', EXTERNAL_MODULE),
]

# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression.
# The latter is currently provided by XZ.
deps = [
    #('ncurses',    local_ncurses_version),
    ('HTSlib',     local_HTSlib_version),
]

#
# Unload modules that are not needed to compile HTSlib. A user has reported crashed with
# version 1.14, so let's remove everything that is not strictly needed.
#
pre_configure_opts = 'module unload rocm cray-libsci xpmem cray-dsmml ; module list ; '
pre_install_opts = pre_test_opts = pre_build_opts = pre_configure_opts

configure_opts = '--with-htslib=$EBROOTHTSLIB --with-ncurses=$EBROOTNCURSES'

post_install_cmds = [
    'mkdir -p %(installdir)s/share/licenses/%(name)s ; cp LICENSE AUTHORS NEWS.md README %(installdir)s/share/licenses/%(name)s'    
]

sanity_check_cmds = [
    'samtools version'
]

env_mod_category = 'bio'

[SAMtools] [package list]