##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/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 local_component of the policy:
# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
##

easyblock = 'Tarball'

name = 'GATK'
version = '3.5'

homepage = 'http://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 local_computing features make it capable of taking on projects of any size."""

toolchain = SYSTEM

# download manually from http://www.broadinstitute.org/gatk/download
sources = ['GenomeAnalysisTK-%(version)s.tar.bz2']

java = 'Java'
javaver = '1.7.0_79'
versionsuffix = '-%s-%s' % (java, javaver)
dependencies = [(java, javaver)]

modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar"""

sanity_check_paths = {
    'files': ["GenomeAnalysisTK.jar"],
    'dirs': ["resources"],
}

moduleclass = 'bio'