From 190335db9c81e44ac61d1c4af71192061a930206 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 Jan 2010 20:50:29 +0000
Subject: [PATCH] Added a GSA specific package with Playground walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2597 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GATK-GSA-Pipeline.xml | 56 ++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 packages/GATK-GSA-Pipeline.xml

diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
new file mode 100644
index 000000000..77fb6025c
--- /dev/null
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- NOTE: Uses playground.
+     ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
+<package>
+  <name>GATK-GSA-Pipeline</name>
+  <executable>
+    <name>GATK-GSA-Pipeline</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <package>org.broadinstitute.sting.gatk.filters</package>
+      <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>
+      <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.HomopolymerCovariate</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.RMSMappingQuality</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
+      <!-- From playground -->
+      <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
+      <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
+    </dependencies>
+  </executable>
+</package>