STAR/2.7.11b-cpeGNU-24.03 (STAR-2.7.11b-cpeGNU-24.03.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 STAR/2.7.11b-cpeGNU-24.03.
EasyConfig:
# Contribution from the NIHR Biomedical Research Centre
# Guy's and St Thomas' NHS Foundation Trust and King's College London
# Based on STAR-2.7.7a-GCC-10.2.0.eb
# uploaded by J. Sassmannshausen
# modified by Thomas Eylenbosch
easyblock = 'MakeCp'
local_STAR_version = '2.7.11b' # https://github.com/alexdobin/STAR/releases
local_zlib_version = '1.3.1' # https://zlib.net/
local_HTSlib_version = '1.19.1' # https://github.com/samtools/htslib/releases
name = 'STAR'
version = '2.7.11b'
homepage = 'https://github.com/alexdobin/STAR'
whatis = [
'Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.',
]
description = """
Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-seq read
mapper, with support for splice-junction and fusion read detection.
STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between
reads (or read pairs) and the genome, using a Suffix Array index. Different
parts of a read can be mapped to different genomic positions, corresponding to
splicing or RNA-fusions. The genome index includes known splice-junctions from
annotated gene models, allowing for sensitive detection of spliced reads. STAR
performs local alignment, automatically soft clipping ends of reads with high
mismatches.
"""
toolchain = {'name': 'cpeGNU', 'version': '24.03'}
toolchainopts = {'openmp': True, 'cstd': 'c++11', 'opt': True} # Mimic the settings that are coded in the Makefile anyway.
# https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11b.tar.gz
sources = {
'download_filename': '%(version)s.tar.gz',
'filename': SOURCE_TAR_GZ,
'source_urls': ['https://github.com/alexdobin/STAR/archive/refs/tags']
}
patches = ['STAR-2.7.11b_use-external-htslib.patch']
checksums = [
{'STAR-2.7.11b.tar.gz': '3f65305e4112bd154c7e22b333dcdaafc681f4a895048fa30fa7ae56cac408e7'},
{'STAR-2.7.11b_use-external-htslib.patch': '4ec4c36d57277adb9b1ea87f2974ebfa0c3b0e3ad1faacd184c5cfe897eb484d'},
]
builddependencies = [
('buildtools', '%(toolchain_version)s', '', SYSTEM), # xxd and other make
]
dependencies = [
('HTSlib', local_HTSlib_version),
('zlib', local_zlib_version),
]
start_dir = 'source'
# by default this is set to -mavx2 which makes it fail on non x86 systems
prebuildopts = 'CXXFLAGS_SIMD= '
buildopts = ' STAR && make STARlong'
files_to_copy = [
(['source/%(name)s', 'source/%(name)slong'], 'bin'),
'doc', 'extras',
(['CHANGES.md', 'LICENSE', 'README.md', 'RELEASEnotes.md'], 'share/licenses/%(name)s'),
]
sanity_check_paths = {
'files': ['bin/%(name)s', 'bin/%(name)slong'],
'dirs': [],
}
sanity_check_commands = [
"STAR --help",
"STARlong --help",
]
moduleclass = 'bio'