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Convert the somatic coverage tool to output from the packaging tool rather than from the dist target. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-18 21:29:30 +00:00
parent 1bca144119
commit af7a759ba4
4 changed files with 13 additions and 41 deletions
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36
build.xml
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@ -110,30 +110,6 @@
</manifest> </manifest>
</jar> </jar>
<jar jarfile="dist/SomaticCoverage.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/somaticcoverage/*.class"/>
<include name="**/walkers/SomaticCoverageWalker.class"/>
</fileset>
<fileset dir="java">
<include name="**/somaticcoverage/*.xml"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool" />
</manifest>
</jar>
<jar jarfile="dist/AnnotateSecondaryBase.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase" />
</manifest>
</jar>
<jar jarfile="dist/Playground.jar" whenmanifestonly="skip"> <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
<fileset dir="build"> <fileset dir="build">
<include name="**/*.class"/> <include name="**/*.class"/>
@ -165,23 +141,11 @@
</manifest> </manifest>
</jar> </jar>
<jar jarfile="dist/AnnotateSecondaryBase.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
<jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip"> <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
<manifest> <manifest>
<attribute name="Class-Path" value="${jar.classpath}"/> <attribute name="Class-Path" value="${jar.classpath}"/>
</manifest> </manifest>
</jar> </jar>
<jar jarfile="dist/SomaticCoverage.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}"/>
</manifest>
</jar>
</target> </target>
<target name="core" description="force a build of the Sting core code"> <target name="core" description="force a build of the Sting core code">

6
java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java
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@ -70,11 +70,7 @@ public class SomaticCoverageTool extends CommandLineExecutable {
/** override any arguments we see fit. */ /** override any arguments we see fit. */
protected void overrideArguments() { protected void overrideArguments() {
try { this.argCollection = GATKArgumentCollection.unmarshal(getClass().getClassLoader().getResourceAsStream("SomaticCoverage.xml"));
this.argCollection = GATKArgumentCollection.unmarshal(this.getClass().getResource("/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml").openStream());
} catch (IOException e) {
throw new RuntimeException(e);
}
this.argCollection.samFiles = samFiles; this.argCollection.samFiles = samFiles;
} }
} }

3
packages/CreatePackager.xsl
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@ -26,6 +26,9 @@
<root classname="{current()}" /> <root classname="{current()}" />
</xsl:for-each> </xsl:for-each>
</classfileset> </classfileset>
<xsl:for-each select="dependencies/file">
<fileset file="{current()}" />
</xsl:for-each>
<manifest> <manifest>
<attribute name="Main-Class" value="{main-class}"/> <attribute name="Main-Class" value="{main-class}"/>
</manifest> </manifest>

9
packages/SomaticCoverage.xml 100644
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@ -0,0 +1,9 @@
<?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>