From ee421c106cf1308f0e70dcd0ab4e3e1d819e4067 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Jan 2010 18:32:46 +0000
Subject: [PATCH] Autogenerate .tar.bz2 with embedded version number.  Misc
 formatting changes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/CreatePackager.xsl    | 38 ++++++++++++++++++++++++----------
 packages/GATK-GSA-Pipeline.xml | 19 ++++++++++-------
 packages/GATK-Picard.xml       | 15 ++++++++------
 packages/GenomeAnalysisTK.xml  | 33 ++++++++++++-----------------
 4 files changed, 60 insertions(+), 45 deletions(-)

diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 9cf2c63e2..15274c7f3 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -6,7 +6,7 @@
   <xsl:variable name="classpath" select="'${sting.dir}/staging:${additional.jars}'" />
   <xsl:variable name="dist.dir" select="'${sting.dir}/dist'" />
   <xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
-  <xsl:variable name="package.dir" select="'${package.dir}/'" />
+  <xsl:variable name="package.dir" select="'${package.dir}'" />
   <xsl:variable name="resources.dir" select="'${package.dir}/resources'" />
 
 <xsl:template match="package">
@@ -16,7 +16,7 @@
 
   <project name="{$project.name}" default="package">
     <property name="sting.dir" value="{$ant.basedir}" />
-    <property name="package.dir" value="{concat($dist.dir,'/packages/',$project.name)}" />
+    <property name="package.dir" value="{$dist.dir}/packages/{$project.name}" />
 
     <target name="package">
       <!-- Verify that all classes specified are present -->
@@ -24,9 +24,9 @@
 	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
 	<fail message="Class {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
-      <xsl:for-each select="//properties">
+      <xsl:for-each select="//resource-bundle">
 	<available property="is.{current()}.present" file="{$staging.dir}/{current()}"/>
-	<fail message="Property file {current()} not found" unless="is.{current()}.present" />
+	<fail message="Resource bundle {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
 
       <!-- Create an output directory for the package -->
@@ -36,7 +36,7 @@
       <xsl:apply-templates select="executable" />
 
       <!-- Add in other modules -->
-      <xsl:for-each select="module">
+      <xsl:for-each select="modules/module">
 	<xsl:apply-templates select="document(current())/package/executable" />
       </xsl:for-each>
 
@@ -53,9 +53,23 @@
         <mkdir dir="{$resources.dir}"/>
         <xsl:call-template name="symlink">
           <xsl:with-param name="file.name" select="." />
-          <xsl:with-param name="target.dir" select="concat($resources.dir,'/')" />
+          <xsl:with-param name="target.dir" select="$resources.dir" />
         </xsl:call-template>
       </xsl:for-each>
+
+      <!-- Bundle the package into a single zip file -->
+      <xsl:choose>
+	<xsl:when test="version">
+	  <property file="{$staging.dir}/{version/@file}" />
+	  <xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
+	  <property name="package.filename" value="{name}-{$version.property}.tar.bz2" />
+	</xsl:when>
+	<xsl:otherwise>
+	  <property name="package.filename" value="{name}.tar.bz2" />
+	</xsl:otherwise>
+      </xsl:choose>
+      <xsl:variable name="package.filename" select="'${package.filename}'" />
+      <tar destfile="{$dist.dir}/{$package.filename}" basedir="{$package.dir}" compression="bzip2" />
     </target>
   </project>
 </xsl:template>
@@ -77,20 +91,21 @@
   </xsl:variable>
   <available property="is.{$short.name}.present" file="{$file.name}"/>
   <fail message="File {$file.name} not found" unless="is.{$short.name}.present" />
-  <delete file="{concat($target.dir,'/',$short.name)}" />
-  <symlink link="{concat($target.dir,'/',$short.name)}" resource="{$full.path}" overwrite="true" />
+  <delete file="{$target.dir}/{$short.name}" />
+  <symlink link="{$target.dir}/{$short.name}" resource="{$full.path}" overwrite="true" />
 </xsl:template>
 
+<!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
 <xsl:template match="executable">
   <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-  <jar jarfile="{concat($package.dir,name,'.jar')}">
+  <jar jarfile="{$package.dir}/{name}.jar">
     <classfileset dir="{$staging.dir}">
       <root classname="{main-class}"/>
     </classfileset>
-    <xsl:for-each select="properties">
+    <xsl:for-each select="resource-bundle">
       <fileset file="{$staging.dir}/{current()}" />
     </xsl:for-each>
-    <xsl:for-each select="module">
+    <xsl:for-each select="modules/module">
       <xsl:apply-templates select="document(current())/package/executable/dependencies" />
     </xsl:for-each>
     <xsl:apply-templates select="dependencies" />
@@ -100,6 +115,7 @@
   </jar>
 </xsl:template>
 
+<!-- Transform a dependency list into a fileset for embedding in a jar -->
 <xsl:template match="dependencies">
   <classfileset dir="{$staging.dir}">
     <xsl:for-each select="package">
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 155e8d660..226077e22 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -3,17 +3,20 @@
      ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
 <package>
   <name>GATK-GSA-Pipeline</name>
+  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
   <executable>
     <name>GATK-GSA-Pipeline</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotator.xml</module>
-    <module>VariantEval.xml</module>
-    <module>FindContaminatingReadGroups.xml</module>
+    <resource-bundle>StingText.properties</resource-bundle>
+    <modules>
+      <module>QualityScoresRecalibration.xml</module>
+      <module>LocalRealignmentAroundIndels.xml</module>
+      <module>UnifiedGenotyper.xml</module>
+      <module>VariantFiltration.xml</module>
+      <module>VariantAnnotator.xml</module>
+      <module>VariantEval.xml</module>
+      <module>FindContaminatingReadGroups.xml</module>
+    </modules>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 1dc8c0877..f43069d9b 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -4,15 +4,18 @@
         Remove the AnalyzeCovariates executable. -->
 <package>
   <name>GATK-Picard</name>
+  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
   <executable>
     <name>GATK-Picard</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotator.xml</module>
+    <resource-bundle>StingText.properties</resource-bundle>
+    <modules>
+      <module>QualityScoresRecalibration.xml</module>
+      <module>LocalRealignmentAroundIndels.xml</module>
+      <module>UnifiedGenotyper.xml</module>
+      <module>VariantFiltration.xml</module>
+      <module>VariantAnnotator.xml</module>
+    </modules>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 18ff53388..8927106b1 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -1,16 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
   <name>GenomeAnalysisTK</name>
+  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
   <executable>
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibration.xml</module>
-    <module>LocalRealignmentAroundIndels.xml</module>
-    <module>UnifiedGenotyper.xml</module>
-    <module>VariantFiltration.xml</module>
-    <module>VariantAnnotator.xml</module>
-    <module>VCFValidator.xml</module>
+    <resource-bundle>StingText.properties</resource-bundle>
+    <modules>
+      <module>QualityScoresRecalibration.xml</module>
+      <module>LocalRealignmentAroundIndels.xml</module>
+      <module>UnifiedGenotyper.xml</module>
+      <module>VariantFiltration.xml</module>
+      <module>VariantAnnotator.xml</module>
+      <module>VCFValidator.xml</module>
+    </modules>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
@@ -23,19 +26,9 @@
       <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</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.QualityScoreCovariate</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>
-    </dependencies>
-  </executable>
+  <modules>
+    <module>AnalyzeCovariates.xml</module>
+  </modules>
   <resources>
     <!-- GATK sample code and build scripts -->
     <file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>