easyblock = 'Tarball'

name = 'GATK'
version = '2.6-5'

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)]

modaliases = {'gatk': "java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar"}

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

moduleclass = 'bio'