60 lines
3.0 KiB
XML
60 lines
3.0 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<package name="GenomeAnalysisTK">
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<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
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<executable name="GenomeAnalysisTK">
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<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
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<resource-bundle file="StingText.properties" />
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<modules>
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<module file="QualityScoresRecalibration.xml" />
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<module file="VariantRecalibration.xml" />
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<module file="LocalRealignmentAroundIndels.xml" />
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<module file="UnifiedGenotyper.xml" />
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<module file="VariantEval.xml" />
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<module file="VariantFiltration.xml" />
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<module file="VariantAnnotator.xml" />
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<module file="IndelGenotyper.xml" />
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</modules>
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<dependencies>
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<!-- Filters -->
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<package name="org.broadinstitute.sting.gatk.filters" />
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<!-- Tribble codecs -->
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<package name="org.broad.tribble.*" />
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<!-- Basic qc walkers -->
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<class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.coverage.DoCOutputMultiplexer" />
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<class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
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<!-- Other misc walkers -->
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<class name="org.broadinstitute.sting.gatk.walkers.sequenom.SequenomValidationConverter" />
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<class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
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<class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
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</dependencies>
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</executable>
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<modules>
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<module file="AnalyzeCovariates.xml"/>
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</modules>
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<resources>
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<!-- GATK sample code and build scripts -->
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
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<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
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<!-- Sample reads and reference files -->
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<file name="testdata/exampleBAM.bam" />
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<file name="testdata/exampleBAM.bam.bai" />
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<file name="testdata/exampleFASTA.fasta" />
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<file name="testdata/exampleFASTA.fasta.fai" />
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<file name="testdata/exampleFASTA.dict" />
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</resources>
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<release>
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<executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
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<archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTK-latest.tar.bz2" />
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</release>
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</package>
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