Bump gatk version to 4.0.4.0. (#7985)
* Bump gatk version to 4.0.4.0. * Update. * Fixed. * Fixed.
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@ -33,23 +33,31 @@ class Gatk(Package):
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"""Genome Analysis Toolkit
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Variant Discovery in High-Throughput Sequencing Data
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"""
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homepage = "http://broadinstitute.github.io/gatk/"
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url = "https://software.broadinstitute.org/gatk/download/auth?package=GATK"
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_urlfmt = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz"
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homepage = "https://software.broadinstitute.org/gatk/"
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url = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
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version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
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url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
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version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
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url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
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depends_on('java@8:', type='run')
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depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
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depends_on('r@3.2:', type='run', when='@4.0:')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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# The list of files to install varies with release...
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# ... but skip the spack-{build.env}.out files.
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files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
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# ... but skip the spack-{build.env}.out files and gatkdoc directory.
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files = [x for x in glob.glob("*")
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if not re.match("^spack-", x) and not re.match("^gatkdoc", x)]
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for f in files:
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install(f, prefix.bin)
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# Skip helper script settings
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if spec.satisfies('@:4.0'):
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return
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
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