Update packaging system to produce multiple jars if asked nicely.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2246 348d0f76-0448-11de-a6fe-93d51630548a

packages/Aligner.xml

@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
+  <name>Aligner</name>
+  <executable>
     <name>Aligner</name>
     <dependencies>
       <!-- BWA/C aligner implementation -->
       <class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
     </dependencies>
+  </executable>
 </package>

packages/AnalyzeCovariates.xml

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <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.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>
-  </dependencies>
-</package>

packages/AnnotateSecondaryBase.xml

@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>AnnotateSecondaryBase</name>
-  <main-class>org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase</main-class>
-</package>

packages/CreatePackager.xsl

@@ -20,7 +20,7 @@
 
     <target name="package">
       <!-- Verify that all classes specified are present -->
-      <xsl:for-each select="dependencies/class">
+      <xsl:for-each select="//class">
 	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
 	<fail message="Class {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
@@ -28,8 +28,9 @@
       <!-- Create an output directory for the package -->
       <mkdir dir="{$package.dir}"/>
 
+      <xsl:for-each select="executable">
 	<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-      <jar jarfile="{concat($package.dir,$project.name,'.jar')}">
+	<jar jarfile="{concat($package.dir,name,'.jar')}">
           <classfileset dir="{$staging.dir}">
             <root classname="{main-class}"/>
             <xsl:for-each select="dependencies/package">
@@ -46,6 +47,7 @@
             <attribute name="Main-Class" value="{main-class}"/>
           </manifest>
 	</jar>
+      </xsl:for-each>
 
       <!-- Include various script files -->
       <xsl:for-each select="scripts/file">

packages/GenomeAnalysisTK.xml

@@ -1,5 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
+  <name>GenomeAnalysisTK</name>
+  <executable>
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <dependencies>
@@ -9,7 +11,7 @@
       <class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</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>
@@ -45,6 +47,23 @@
       <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
       <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</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.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>
+    </dependencies>
+  </executable>
   <resources>
     <!-- GATK sample code and build scripts -->
     <file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
@@ -52,7 +71,7 @@
     <file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
+    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
     <!-- Sample reads and reference files -->

packages/PicardPrivate.xml

@@ -1,5 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
+  <name>picard-private-parts</name>
+  <executable>
     <name>picard-private-parts</name>
     <dependencies>
       <class>edu.mit.broad.picard.directed.IntervalList</class>
@@ -26,4 +28,5 @@
       <class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
       <class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
     </dependencies>
+  </executable>
 </package>

packages/SomaticCoverage.xml

@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>SomaticCoverage</name>
-  <main-class>org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool</main-class>
-  <dependencies>
-    <class>org.broadinstitute.sting.playground.gatk.walkers.SomaticCoverageWalker</class>
-    <file>java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml</file>
-  </dependencies>
-</package>

packages/VCFValidator.xml

@@ -1,5 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
+  <name>VCFValidator</name>
+  <executable>
     <name>VCFValidator</name>
     <main-class>org.broadinstitute.sting.utils.genotype.vcf.VCFValidator</main-class>
+  </executable>
 </package>