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Minor build.xml cleanup post-variant-migration 

-Stop emitting our own (now empty) variant jar
-Correct BaseUtils package for the na12878kb jar
This commit is contained in:
David Roazen 2013-02-06 11:15:03 -05:00
parent bd0349e570
commit df142a389f
1 changed files with 2 additions and 10 deletions
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12
build.xml
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@ -669,21 +669,13 @@
</jar> </jar>
</target> </target>
<target name="variant.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/variant.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/variant/**/*.class"/>
</fileset>
</jar>
</target>
<target name="na12878kb.jar" depends="gatk.compile,init.jar"> <target name="na12878kb.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/na12878kb.jar"> <jar jarfile="${dist.dir}/na12878kb.jar">
<fileset dir="${java.classes}"> <fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/> <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
<include name="org/broadinstitute/sting/utils/GenomeLoc.class"/> <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
<include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/> <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
<include name="org/broadinstitute/variant/utils/BaseUtils.class"/> <include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
<include name="org/broadinstitute/sting/utils/Utils.class"/> <include name="org/broadinstitute/sting/utils/Utils.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/> <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/> <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
@ -753,7 +745,7 @@
</jar> </jar>
</target> </target>
<target name="sting.jar" depends="sting-utils.jar, variant.jar, gatk.jar, queue.jar" /> <target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
<target name="init.manifests" depends="sting.jar"> <target name="init.manifests" depends="sting.jar">
<pathconvert property="jar.classpath" pathsep=" "> <pathconvert property="jar.classpath" pathsep=" ">