From 4b17f346409ff56c2192f60d311b03d69f5f6b89 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Thu, 30 Jun 2011 18:27:17 -0400
Subject: [PATCH] Fixes to the packaging system to work with the new directory
 structure. Also added a few R scripts to the list of files to include in the
 resources directory of the binary distribution, at Ryan's request.

---
 build.xml                             |  6 +++---
 public/packages/AnalyzeCovariates.xml |  4 ++--
 public/packages/GATKEngine.xml        | 10 +++++-----
 public/packages/GenomeAnalysisTK.xml  | 15 +++++++++------
 4 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/build.xml b/build.xml
index cf8623bed..fe1723587 100644
--- a/build.xml
+++ b/build.xml
@@ -64,7 +64,7 @@
     <property name="usefile" value="false" />
 
     <!-- If running the 'package' task, this property controls the name of the xml file to package -->
-    <property name="package.xml.dir" value="packages" />
+    <property name="package.xml.dir" value="${public.dir}/packages" />
     <property name="executable" value="GenomeAnalysisTK" />
 
     <property environment="env"/>
@@ -896,7 +896,7 @@
     <!-- Build a package consisting of all supporting files -->
     <target name="package" depends="dist,stage" description="bundle up an executable for distribution">
       <mkdir dir="dist/packages" />
-      <xslt destdir="dist/packages" style="packages/CreatePackager.xsl" useImplicitFileset="false">
+      <xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
           <flattenmapper/>
           <fileset dir="${package.xml.dir}">
               <include name="${executable}.xml" />
@@ -934,7 +934,7 @@
 
       <!-- Use the packaging system to extract parts of picard-private we need -->
       <mkdir dir="${dist.dir}/packages" />
-      <xslt in="packages/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
+      <xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
       <ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
 	    <property name="additional.jars" value="${required.picard.jars}" />
       </ant>
diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
index 3a3cae54e..1862d6cbb 100644
--- a/public/packages/AnalyzeCovariates.xml
+++ b/public/packages/AnalyzeCovariates.xml
@@ -15,7 +15,7 @@
   </executable>
   <resources>
     <!-- Supplemental scripts for graph generation, etc. -->
-    <file name="R/plot_residualError_OtherCovariate.R" />
-    <file name="R/plot_residualError_QualityScoreCovariate.R" />
+    <file name="public/R/plot_residualError_OtherCovariate.R" />
+    <file name="public/R/plot_residualError_QualityScoreCovariate.R" />
   </resources>
 </package>
diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index 1f35522d9..4f635f7fb 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -40,10 +40,10 @@
   </executable>
   <resources>
     <!-- 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" />
+    <file name="public/testdata/exampleBAM.bam" />
+    <file name="public/testdata/exampleBAM.bam.bai" />
+    <file name="public/testdata/exampleFASTA.fasta" />
+    <file name="public/testdata/exampleFASTA.fasta.fai" />
+    <file name="public/testdata/exampleFASTA.dict" />
   </resources>
 </package>
diff --git a/public/packages/GenomeAnalysisTK.xml b/public/packages/GenomeAnalysisTK.xml
index 2aa58952e..f923ea698 100644
--- a/public/packages/GenomeAnalysisTK.xml
+++ b/public/packages/GenomeAnalysisTK.xml
@@ -13,12 +13,15 @@
   </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="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
+    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
+    <file name="public/R/plot_Annotations_BinnedTruthMetrics.R" />
+    <file name="public/R/plot_Tranches.R" />
+    <file name="public/R/titvFPEst.R" />
   </resources>
   <release>
     <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />