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Create package that contains just what Picard needs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2421 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
alecw 2009-12-21 18:48:27 +00:00
parent e06dfe44c4
commit c0c9f6c8b6
1 changed files with 8 additions and 20 deletions
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28
packages/GATK-Picard.xml
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@ -1,4 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- In order to update this file, copy GenomeAnalysisTK.xml, change the name of the
package and executable to GATK-Picard, and add TileCovariate to the list of dependencies.
Remove the AnalyzeCovariates executable. -->
<package>
<name>GATK-Picard</name>
<executable>
@ -6,11 +9,11 @@
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
@ -25,6 +28,7 @@
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
<!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
@ -48,29 +52,13 @@
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
</dependencies>
</executable>
<executable>
<name>AnalyzeCovariates</name>
<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
<dependencies>
<!-- Recalibration analysis script -->
<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
</dependencies>
</executable>
<resources>
<!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>