GATK-4.0.3.0-Java-1.8.0_144.eb 1.23 KB
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# IT4Innovations 2018

easyblock = 'Tarball'

name = 'GATK'
version = '4.0.3.0'
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 computing features make it capable of taking on projects of any size."""

toolchain = {'name': 'dummy', 'version': ''}

# 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_144')]


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

modextravars = {
    'export GATK_LOCAL_JAR':'%(installdir)s/gatk-package-4.0.3.0-local.jar'
}

sanity_check_paths = {
    'files': ['gatk-package-4.0.3.0-local.jar', 'gatk-package-4.0.3.0-spark.jar'],
    'dirs': ['bin'],
}

moduleclass = 'bio'