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gatk-3.8
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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
This commit is contained in:
hanna 2009-12-03 17:11:12 +00:00
parent 01cf5cc741
commit 608fa4cc3a
8 changed files with 123 additions and 124 deletions
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11
packages/Aligner.xml
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@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<package> <package>
<name>Aligner</name> <name>Aligner</name>
<dependencies> <executable>
<!-- BWA/C aligner implementation --> <name>Aligner</name>
<class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class> <dependencies>
</dependencies> <!-- BWA/C aligner implementation -->
<class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
</dependencies>
</executable>
</package> </package>

17
packages/AnalyzeCovariates.xml
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@ -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>

5
packages/AnnotateSecondaryBase.xml
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@ -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>

38
packages/CreatePackager.xsl
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@ -20,7 +20,7 @@
<target name="package"> <target name="package">
<!-- Verify that all classes specified are present --> <!-- Verify that all classes specified are present -->
<xsl:for-each select="dependencies/class"> <xsl:for-each select="//class">
<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/> <available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
<fail message="Class {current()} not found" unless="is.{current()}.present" /> <fail message="Class {current()} not found" unless="is.{current()}.present" />
</xsl:for-each> </xsl:for-each>
@ -28,24 +28,26 @@
<!-- Create an output directory for the package --> <!-- Create an output directory for the package -->
<mkdir dir="{$package.dir}"/> <mkdir dir="{$package.dir}"/>
<!-- Create a jar file containing the specified classes / packages and all their dependencies --> <xsl:for-each select="executable">
<jar jarfile="{concat($package.dir,$project.name,'.jar')}"> <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
<classfileset dir="{$staging.dir}"> <jar jarfile="{concat($package.dir,name,'.jar')}">
<root classname="{main-class}"/> <classfileset dir="{$staging.dir}">
<xsl:for-each select="dependencies/package"> <root classname="{main-class}"/>
<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" /> <xsl:for-each select="dependencies/package">
<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
</xsl:for-each>
<xsl:for-each select="dependencies/class">
<root classname="{current()}" />
</xsl:for-each>
</classfileset>
<xsl:for-each select="dependencies/file">
<fileset file="{current()}" />
</xsl:for-each> </xsl:for-each>
<xsl:for-each select="dependencies/class"> <manifest>
<root classname="{current()}" /> <attribute name="Main-Class" value="{main-class}"/>
</xsl:for-each> </manifest>
</classfileset> </jar>
<xsl:for-each select="dependencies/file"> </xsl:for-each>
<fileset file="{current()}" />
</xsl:for-each>
<manifest>
<attribute name="Main-Class" value="{main-class}"/>
</manifest>
</jar>
<!-- Include various script files --> <!-- Include various script files -->
<xsl:for-each select="scripts/file"> <xsl:for-each select="scripts/file">

109
packages/GenomeAnalysisTK.xml
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@ -1,50 +1,69 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<package> <package>
<name>GenomeAnalysisTK</name> <name>GenomeAnalysisTK</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <executable>
<dependencies> <name>GenomeAnalysisTK</name>
<package>org.broadinstitute.sting.gatk.filters</package> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class> <dependencies>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class> <package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class> <class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class> <class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class> <class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class> <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<!-- Quality scores recalibration --> <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class> <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class> <!-- Quality scores recalibration -->
<!-- Recalibration Covariates --> <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class> <!-- Recalibration Covariates -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<!-- Local realignment around indels --> <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class> <!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class> <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
<!-- Unified genotyper --> <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class> <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
<!-- Variant filtration --> <!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class> <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
<!-- Variant annotator --> <!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class> <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
<!-- And the annotations --> <!-- Variant annotator -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class> <!-- And the annotations -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
</dependencies> <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> <resources>
<!-- GATK sample code and build scripts --> <!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file> <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/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.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/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/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file> <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
<!-- Sample reads and reference files --> <!-- Sample reads and reference files -->

53
packages/PicardPrivate.xml
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@ -1,29 +1,32 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<package> <package>
<name>picard-private-parts</name> <name>picard-private-parts</name>
<dependencies> <executable>
<class>edu.mit.broad.picard.directed.IntervalList</class> <name>picard-private-parts</name>
<class>edu.mit.broad.picard.genotype.DiploidGenotype</class> <dependencies>
<class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class> <class>edu.mit.broad.picard.directed.IntervalList</class>
<class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class> <class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
<class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class> <class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
<class>edu.mit.broad.picard.util.BasicTextFileParser</class> <class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
<class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class> <class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
<class>edu.mit.broad.picard.util.Interval</class> <class>edu.mit.broad.picard.util.BasicTextFileParser</class>
<class>edu.mit.broad.picard.util.IntervalTree</class> <class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
<class>edu.mit.broad.picard.util.OverlapDetector</class> <class>edu.mit.broad.picard.util.Interval</class>
<class>edu.mit.broad.picard.util.PasteParser</class> <class>edu.mit.broad.picard.util.IntervalTree</class>
<class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class> <class>edu.mit.broad.picard.util.OverlapDetector</class>
<class>edu.mit.broad.picard.variation.KnownVariantCodec</class> <class>edu.mit.broad.picard.util.PasteParser</class>
<class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class> <class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
<class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class> <class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
<class>edu.mit.broad.picard.variation.VariantType</class> <class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
<class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class> <class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
<class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class> <class>edu.mit.broad.picard.variation.VariantType</class>
<class>edu.mit.broad.picard.variation.KnownVariantIterator</class> <class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
<class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class> <class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
<class>edu.mit.broad.picard.variation.KnownVariant</class> <class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
<class>edu.mit.broad.picard.variation.DbSnpFileReader</class> <class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
<class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class> <class>edu.mit.broad.picard.variation.KnownVariant</class>
</dependencies> <class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
<class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
</dependencies>
</executable>
</package> </package>

9
packages/SomaticCoverage.xml
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@ -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>

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