From 2cf21317f97ced2df3f963e2205971ade682cbfb Mon Sep 17 00:00:00 2001
From: alecw <alecw@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 7 Dec 2009 21:22:07 +0000
Subject: [PATCH] Create package that contains just what Picard needs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2282 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GATK-Picard.xml | 88 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 packages/GATK-Picard.xml

diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
new file mode 100644
index 000000000..c830b60d2
--- /dev/null
+++ b/packages/GATK-Picard.xml
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>GATK-Picard</name>
+  <executable>
+    <name>GATK-Picard</name>
+    <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.ValidatingPileupWalker</class>
+      <!-- Quality scores recalibration -->
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
+      <!-- Recalibration Covariates -->
+      <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>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
+      <!-- Local realignment around indels -->
+      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
+      <!-- Unified genotyper -->
+      <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
+      <!-- Variant filtration -->
+      <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
+      <!-- Variant annotator -->
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
+      <!-- And the annotations -->
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
+      <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/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>
+    <!-- Sample reads and reference files -->
+    <file>testdata/exampleBAM.bam</file>
+    <file>testdata/exampleBAM.bam.bai</file>
+    <file>testdata/exampleFASTA.fasta</file>
+    <file>testdata/exampleFASTA.fasta.fai</file>
+    <file>testdata/exampleFASTA.dict</file>
+    <!-- Supplemental scripts for graph generation, etc. -->
+    <file>R/plot_residualError_OtherCovariate.R</file>
+    <file>R/plot_residualError_QualityScoreCovariate.R</file>
+  </resources>
+</package>