# IT4Innovations 2019

easyblock = 'Tarball'

name = 'GATK'
version = '4.1.2.0'
versionsuffix = '-Java-%(javaver)s'

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

sources = ['gatk-%(version)s.zip']

dependencies = [('Java', '1.8.0_202')]


postinstallcmds = [
    'mkdir %(installdir)s/bin',
    'mv %(installdir)s/gatk %(installdir)s/bin',
]

modextravars = {
    'export GATK_LOCAL_JAR': '%(installdir)s/gatk-package-%(version)s-local.jar'
}

sanity_check_paths = {
    'files': [
        'gatk-package-%(version)s-local.jar',
        'gatk-package-%(version)s-spark.jar'],
    'dirs': ['bin'],
}

moduleclass = 'bio'