<?xml version="1.0" encoding="UTF-8"?>
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  ~
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  ~ obtaining a copy of this software and associated documentation
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  ~ copies of the Software, and to permit persons to whom the
  ~ Software is furnished to do so, subject to the following
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<package name="GATKEngine">
  <executable name="GATKEngine">
    <dependencies>
      <!-- Package everything in org.broadinstitute.sting -->
      <package name="org.broadinstitute.sting.**" />
      <!-- Tribble codecs -->
      <package name="org.broad.tribble.**" />
      <!-- Workaround - depend on the logger impl required by JEXL -->
      <package name="org.apache.commons.logging.impl" />
      <!-- R packages -->
      <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
      <!-- All R scripts in org.broadinstitute.sting -->
      <dir name="org/broadinstitute/sting" includes="**/*.R" />
      <!-- The GATK public key -->
      <file path="GATK_public.key" />
    </dependencies>
  </executable>
  <resources>
    <!-- Sample reads and reference files -->
    <file name="public/testdata/exampleBAM.bam" />
    <file name="public/testdata/exampleBAM.bam.bai" />
    <file name="public/testdata/exampleFASTA.fasta" />
    <file name="public/testdata/exampleFASTA.fasta.fai" />
    <file name="public/testdata/exampleFASTA.dict" />
  </resources>
</package>
