easyblock = 'Tarball'

name = 'GATK'
version = '2.7-4'

homepage = 'http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit'
description = """The GATK is a structured software library that makes writing efficient analysis tools
 using next-generation sequencing data very easy, and second it's a suite of tools for working with human
 medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things
 like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner."""

toolchain = SYSTEM

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

dependencies = [('Java', '1.7.0_10')]

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

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

moduleclass = 'bio'