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Fixes to the packaging system to work with the new directory structure. 

Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
This commit is contained in:
David Roazen 2011-06-30 18:27:17 -04:00
parent 5786b51bcf
commit 4b17f34640
4 changed files with 19 additions and 16 deletions
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6
build.xml
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@ -64,7 +64,7 @@
<property name="usefile" value="false" />
<!-- If running the 'package' task, this property controls the name of the xml file to package -->
<property name="package.xml.dir" value="packages" />
<property name="package.xml.dir" value="${public.dir}/packages" />
<property name="executable" value="GenomeAnalysisTK" />
<property environment="env"/>
@ -896,7 +896,7 @@
<!-- Build a package consisting of all supporting files -->
<target name="package" depends="dist,stage" description="bundle up an executable for distribution">
<mkdir dir="dist/packages" />
<xslt destdir="dist/packages" style="packages/CreatePackager.xsl" useImplicitFileset="false">
<xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/>
<fileset dir="${package.xml.dir}">
<include name="${executable}.xml" />
@ -934,7 +934,7 @@
<!-- Use the packaging system to extract parts of picard-private we need -->
<mkdir dir="${dist.dir}/packages" />
<xslt in="packages/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
<property name="additional.jars" value="${required.picard.jars}" />
</ant>

4
public/packages/AnalyzeCovariates.xml
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@ -15,7 +15,7 @@
</executable>
<resources>
<!-- Supplemental scripts for graph generation, etc. -->
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
<file name="public/R/plot_residualError_OtherCovariate.R" />
<file name="public/R/plot_residualError_QualityScoreCovariate.R" />
</resources>
</package>

10
public/packages/GATKEngine.xml
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@ -40,10 +40,10 @@
</executable>
<resources>
<!-- Sample reads and reference files -->
<file name="testdata/exampleBAM.bam" />
<file name="testdata/exampleBAM.bam.bai" />
<file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" />
<file name="public/testdata/exampleBAM.bam" />
<file name="public/testdata/exampleBAM.bam.bai" />
<file name="public/testdata/exampleFASTA.fasta" />
<file name="public/testdata/exampleFASTA.fasta.fai" />
<file name="public/testdata/exampleFASTA.dict" />
</resources>
</package>

15
public/packages/GenomeAnalysisTK.xml
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@ -13,12 +13,15 @@
</modules>
<resources>
<!-- GATK sample code and build scripts -->
<file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
<file name="public/R/plot_Annotations_BinnedTruthMetrics.R" />
<file name="public/R/plot_Tranches.R" />
<file name="public/R/titvFPEst.R" />
</resources>
<release>
<executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />