gatk: updating and expanding java dependency (#30476)
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@ -15,7 +15,9 @@ class Gatk(Package):
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homepage = "https://gatk.broadinstitute.org/hc/en-us"
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url = "https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip"
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list_url = "https://github.com/broadinstitute/gatk/releases"
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maintainers = ['snehring']
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version('4.2.6.1', sha256='1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628')
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version('4.2.2.0', sha256='ddd902441d1874493796566159288e9df178714ac18216ba05092136db1497fd')
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version('4.1.8.1', sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc")
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version('4.1.8.0', sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6")
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@ -48,7 +50,7 @@ class Gatk(Package):
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# output.
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variant('r', default=False, description='Use R for plotting')
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depends_on("java@8", type="run")
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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: +r")
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@ -62,6 +64,7 @@ def install(self, spec, prefix):
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# Skip helper script for versions >4.0
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if spec.satisfies("@4.0:"):
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set_executable('gatk')
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install("gatk", prefix.bin)
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else:
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# Set up a helper script to call java on the jar file,
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