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new file: b/Boost/Boost-1.68.0-intel-2017a.eb new file: b/Boost/Boost-1.68.0-intel-2017c.eb new file: "b/bcl2fastq2/\\" new file: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-2.7.eb new file: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-3.6.eb modified: d/DIRAC/DIRAC-18.0-intel-2017c-Py-2.7-test.eb new file: f/FastQC/FastQC-0.11.3.eb new file: f/FastQC/FastQC-0.11.8.eb new file: f/fontconfig/fontconfig-2.13.0-libpng-1.6.34.eb new file: g/GATK/GATK-4.1.2.0-Java-1.8.0_202.eb new file: g/GDAL/GDAL-2.4.0-intel-2017a-Py-3.6.eb new file: g/GEOS/GEOS-3.7.2-Py-3.6.eb new file: g/gnuplot/gnuplot-5.2.7-GCC-6.3.0-2.27.eb modified: h/HTSlib/HTSlib-1.6-intel-2017a.eb new file: l/libMesh/libMesh-1.4.1-intel-2017a.eb new file: l/libMesh/libMesh-1.4.1-intel-2017c.eb new file: m/MUMPS/MUMPS-5.2.0-intel-2017c-parmetis.eb modified: p/Python/Python-3.6.8-GCC-6.3.0-2.27-base.eb new file: r/R/R-3.5.3-intel-2017a-Py-3.6.eb modified: s/SAMtools/SAMtools-1.6-intel-2017a.eb new file: s/SWIG/SWIG-3.0.12-Py-3.6.eb deleted: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Python-2.7.13.eb
44 lines
1.3 KiB
Plaintext
44 lines
1.3 KiB
Plaintext
# IT4Innovations 2019
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easyblock = 'Tarball'
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name = 'GATK'
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version = '4.1.2.0'
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versionsuffix = '-Java-%(javaver)s'
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homepage = 'http://www.broadinstitute.org/gatk/'
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description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
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to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
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with a primary focus on variant discovery and genotyping as well as strong emphasis on
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data quality assurance. Its robust architecture, powerful processing engine and
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high-performance computing features make it capable of taking on projects of any size."""
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toolchain = {'name': 'dummy', 'version': ''}
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# download manually from http://www.broadinstitute.org/gatk/download
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source_urls = [
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' https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
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sources = ['gatk-%(version)s.zip']
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dependencies = [('Java', '1.8.0_202')]
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postinstallcmds = [
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'mkdir %(installdir)s/bin',
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'mv %(installdir)s/gatk %(installdir)s/bin',
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]
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modextravars = {
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'export GATK_LOCAL_JAR': '%(installdir)s/gatk-package-%(version)s-local.jar'
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}
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sanity_check_paths = {
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'files': [
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'gatk-package-%(version)s-local.jar',
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'gatk-package-%(version)s-spark.jar'],
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'dirs': ['bin'],
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}
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moduleclass = 'bio'
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