From 4fc926232cb9076854a8484cdd81ccef2595bdb0 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Jan 2010 19:38:46 +0000
Subject: [PATCH] More cleanup.  Make sure resources are unioned among all the
 specified modules.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2653 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/AnalyzeCovariates.xml |  5 +++++
 packages/CreatePackager.xsl    | 30 +++++++++++++++---------------
 packages/GATK-Picard.xml       |  3 ---
 packages/GenomeAnalysisTK.xml  |  3 ---
 4 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/packages/AnalyzeCovariates.xml b/packages/AnalyzeCovariates.xml
index 1ad7be3d7..87f055f83 100644
--- a/packages/AnalyzeCovariates.xml
+++ b/packages/AnalyzeCovariates.xml
@@ -13,4 +13,9 @@
       <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
+  <resources>
+    <!-- Supplemental scripts for graph generation, etc. -->
+    <file name="R/plot_residualError_OtherCovariate.R" />
+    <file name="R/plot_residualError_QualityScoreCovariate.R" />
+  </resources>
 </package>
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 38f3f9004..f28144cbb 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -40,21 +40,10 @@
 	<xsl:apply-templates select="document(@file)/package/executable" />
       </xsl:for-each>
 
-      <!-- Include various script files -->
-      <xsl:for-each select="scripts/file">
-        <xsl:call-template name="symlink">
-          <xsl:with-param name="file.name" select="@name" />
-          <xsl:with-param name="target.dir" select="$package.dir" />
-        </xsl:call-template>
-      </xsl:for-each>
-
-      <!-- Include various resource files -->
-      <xsl:for-each select="resources/file">
-        <mkdir dir="{$resources.dir}"/>
-        <xsl:call-template name="symlink">
-          <xsl:with-param name="file.name" select="@name" />
-          <xsl:with-param name="target.dir" select="$resources.dir" />
-        </xsl:call-template>
+      <!-- Include various resource files explicitly specified in this file and in all other modules -->
+      <xsl:apply-templates select="resources" />
+      <xsl:for-each select="//modules/module">
+	<xsl:apply-templates select="document(@file)/package/resources" />
       </xsl:for-each>
 
       <!-- Bundle the package into a single zip file -->
@@ -115,6 +104,17 @@
   </jar>
 </xsl:template>
 
+<!-- Transform a resource file into a symlink operation -->
+<xsl:template match="resources">
+  <xsl:for-each select="file">
+    <mkdir dir="{$resources.dir}"/>
+    <xsl:call-template name="symlink">
+      <xsl:with-param name="file.name" select="@name" />
+      <xsl:with-param name="target.dir" select="$resources.dir" />
+    </xsl:call-template>
+  </xsl:for-each>
+</xsl:template>
+
 <!-- Transform a dependency list into a fileset for embedding in a jar -->
 <xsl:template match="dependencies">
   <classfileset dir="{$staging.dir}">
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index ae04f9177..207e2c0a6 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -47,8 +47,5 @@
     <file name="testdata/exampleFASTA.fasta" />
     <file name="testdata/exampleFASTA.fasta.fai" />
     <file name="testdata/exampleFASTA.dict" />
-    <!-- Supplemental scripts for graph generation, etc. -->
-    <file name="R/plot_residualError_OtherCovariate.R" />
-    <file name="R/plot_residualError_QualityScoreCovariate.R" />
   </resources>
 </package>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 4ae5d6819..933089b60 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -43,8 +43,5 @@
     <file name="testdata/exampleFASTA.fasta" />
     <file name="testdata/exampleFASTA.fasta.fai" />
     <file name="testdata/exampleFASTA.dict" />
-    <!-- Supplemental scripts for graph generation, etc. -->
-    <file name="R/plot_residualError_OtherCovariate.R" />
-    <file name="R/plot_residualError_QualityScoreCovariate.R" />
   </resources>
 </package>