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GRIDSS-2.12.0-foss-2020b.eb
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GRIDSS-2.12.0-foss-2020b.eb
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# #
# This is a contribution from HPCNow! (http://hpcnow.com)
# Copyright:: HPCNow!
# Authors:: Jordi Blasco <jordi.blasco@hpcnow.com>
# License:: GPL-v3.0
# #
easyblock = 'BinariesTarball'
name = 'GRIDSS'
version = '2.12.0'
homepage = 'https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation'
description = """GRIDSS is a module software suite containing tools useful for
the detection of genomic rearrangements. GRIDSS includes a genome-wide
break-end assembler, as well as a structural variation caller for Illumina
sequencing data. GRIDSS calls variants based on alignment-guided positional de
Bruijn graph genome-wide break-end assembly, split read, and read pair
evidence."""
toolchain = {'name': 'foss', 'version': '2020b'}
github_account = 'PapenfussLab'
source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['5f00c918804a4e0cbe7dd8c61963058841f2104a01c58fc34bc19a0cc8c1a763']
dependencies = [
('Java', '11', '', True),
('R', '4.0.4'),
('SAMtools', '1.11'),
('BWA', '0.7.17'),
('picard', '2.25.0', '', ('Java', '11')),
]
sanity_check_paths = {
'files': ['bin/gridss', 'bin/gridss-%(version)s-gridss-jar-with-dependencies.jar', 'bin/gridss.config.R'],
'dirs': ['bin'],
}
sanity_check_commands = ["gridss --help 2>&1 | grep '^Usage:'"]
modextrapaths = {
'GRIDSS_JAR': ['bin'],
}
moduleclass = 'bio'