##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB
# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>,
#             Kenneth Hoste (UGent)
# License::   MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
# Modified by: Adam Huffman, Jonas Demeulemeester
# The Francis Crick Institute
# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen
##

easyblock = 'Tarball'

name = 'GATK'
version = '4.1.9.0'
versionsuffix = '-Java-%(javaver)s'

homepage = 'https://www.broadinstitute.org/gatk/'
description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
 to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
 with a primary focus on variant discovery and genotyping as well as strong emphasis on
 data quality assurance. Its robust architecture, powerful processing engine and
 high-performance computing features make it capable of taking on projects of any size."""

toolchain = {'name': 'GCCcore', 'version': '10.2.0'}

source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
sources = ['gatk-%(version)s.zip']

dependencies = [
    ('Java', '11', '', True),
    ('Python', '3.8.6'),
]

modextrapaths = {'PATH': ''}

sanity_check_paths = {
    'files': ['gatk'],
    'dirs': [],
}
sanity_check_commands = [
    "gatk --help",
    "gatk --list",
]

# modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n"

moduleclass = 'bio'
