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