From 96a053c76933a2ec07a07adef5c22e4452fe1560 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 22:10:33 +0000
Subject: [PATCH] Port VariantEval and FindContaminatingReadGroups to modules.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2634 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/FindContaminatingReadGroupsModule.xml | 11 +++++++++++
 packages/GATK-GSA-Pipeline.xml                 |  5 ++---
 packages/VariantEvalModule.xml                 | 11 +++++++++++
 3 files changed, 24 insertions(+), 3 deletions(-)
 create mode 100644 packages/FindContaminatingReadGroupsModule.xml
 create mode 100644 packages/VariantEvalModule.xml

diff --git a/packages/FindContaminatingReadGroupsModule.xml b/packages/FindContaminatingReadGroupsModule.xml
new file mode 100644
index 000000000..279524a22
--- /dev/null
+++ b/packages/FindContaminatingReadGroupsModule.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>FindContaminatingReadGroups</name>
+  <executable>
+    <name>FindContaminatingReadGroups</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index ac37491e7..4d259b64d 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -12,12 +12,11 @@
     <module>UnifiedGenotyperModule.xml</module>
     <module>VariantFiltrationModule.xml</module>
     <module>VariantAnnotatorModule.xml</module>
+    <module>VariantEvalModule.xml</module>
+    <module>FindContaminatingReadGroupsModule.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
-      <!-- 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>
diff --git a/packages/VariantEvalModule.xml b/packages/VariantEvalModule.xml
new file mode 100644
index 000000000..2cabda8ce
--- /dev/null
+++ b/packages/VariantEvalModule.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>VariantEval</name>
+  <executable>
+    <name>VariantEval</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
+    </dependencies>
+  </executable>
+</package>