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
parent
01cf5cc741
commit
608fa4cc3a
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@ -1,8 +1,11 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>Aligner</name>
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<dependencies>
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<!-- BWA/C aligner implementation -->
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<class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
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</dependencies>
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<executable>
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<name>Aligner</name>
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<dependencies>
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<!-- BWA/C aligner implementation -->
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<class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
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</dependencies>
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</executable>
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</package>
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@ -1,17 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>AnalyzeCovariates</name>
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<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
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<dependencies>
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<!-- Recalibration analysis script -->
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<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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</dependencies>
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</package>
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@ -1,5 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>AnnotateSecondaryBase</name>
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<main-class>org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase</main-class>
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</package>
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@ -20,7 +20,7 @@
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<target name="package">
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<!-- Verify that all classes specified are present -->
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<xsl:for-each select="dependencies/class">
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<xsl:for-each select="//class">
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<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
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<fail message="Class {current()} not found" unless="is.{current()}.present" />
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</xsl:for-each>
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@ -28,24 +28,26 @@
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<!-- Create an output directory for the package -->
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<mkdir dir="{$package.dir}"/>
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<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
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<jar jarfile="{concat($package.dir,$project.name,'.jar')}">
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<classfileset dir="{$staging.dir}">
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<root classname="{main-class}"/>
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<xsl:for-each select="dependencies/package">
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<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
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<xsl:for-each select="executable">
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<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
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<jar jarfile="{concat($package.dir,name,'.jar')}">
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<classfileset dir="{$staging.dir}">
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<root classname="{main-class}"/>
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<xsl:for-each select="dependencies/package">
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<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
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</xsl:for-each>
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<xsl:for-each select="dependencies/class">
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<root classname="{current()}" />
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</xsl:for-each>
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</classfileset>
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<xsl:for-each select="dependencies/file">
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<fileset file="{current()}" />
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</xsl:for-each>
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<xsl:for-each select="dependencies/class">
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<root classname="{current()}" />
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</xsl:for-each>
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</classfileset>
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<xsl:for-each select="dependencies/file">
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<fileset file="{current()}" />
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</xsl:for-each>
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<manifest>
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<attribute name="Main-Class" value="{main-class}"/>
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</manifest>
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</jar>
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<manifest>
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<attribute name="Main-Class" value="{main-class}"/>
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</manifest>
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</jar>
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</xsl:for-each>
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<!-- Include various script files -->
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<xsl:for-each select="scripts/file">
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@ -1,50 +1,69 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>GenomeAnalysisTK</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<dependencies>
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<package>org.broadinstitute.sting.gatk.filters</package>
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<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class>
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<!-- Quality scores recalibration -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
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<!-- Recalibration Covariates -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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<!-- Local realignment around indels -->
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<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
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<!-- Unified genotyper -->
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<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
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<!-- Variant filtration -->
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<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
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<!-- Variant annotator -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
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<!-- And the annotations -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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</dependencies>
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<executable>
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<name>GenomeAnalysisTK</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<dependencies>
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<package>org.broadinstitute.sting.gatk.filters</package>
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<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
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<!-- Quality scores recalibration -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
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<!-- Recalibration Covariates -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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<!-- Local realignment around indels -->
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<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
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<!-- Unified genotyper -->
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<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
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<!-- Variant filtration -->
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<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
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<!-- Variant annotator -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
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<!-- And the annotations -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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</dependencies>
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</executable>
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<executable>
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<name>AnalyzeCovariates</name>
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<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
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<dependencies>
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<!-- Recalibration analysis script -->
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<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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</dependencies>
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</executable>
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<resources>
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<!-- GATK sample code and build scripts -->
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<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
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@ -52,7 +71,7 @@
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<file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
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<!-- Sample reads and reference files -->
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@ -1,29 +1,32 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>picard-private-parts</name>
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<dependencies>
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<class>edu.mit.broad.picard.directed.IntervalList</class>
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<class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
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<class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
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<class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
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<class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
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<class>edu.mit.broad.picard.util.BasicTextFileParser</class>
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<class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
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<class>edu.mit.broad.picard.util.Interval</class>
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<class>edu.mit.broad.picard.util.IntervalTree</class>
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<class>edu.mit.broad.picard.util.OverlapDetector</class>
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<class>edu.mit.broad.picard.util.PasteParser</class>
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<class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
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<class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
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<class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
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<class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
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<class>edu.mit.broad.picard.variation.VariantType</class>
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<class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
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<class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
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<class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
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<class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
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<class>edu.mit.broad.picard.variation.KnownVariant</class>
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<class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
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<class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
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</dependencies>
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<executable>
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<name>picard-private-parts</name>
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<dependencies>
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<class>edu.mit.broad.picard.directed.IntervalList</class>
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<class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
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<class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
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<class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
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<class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
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<class>edu.mit.broad.picard.util.BasicTextFileParser</class>
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<class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
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<class>edu.mit.broad.picard.util.Interval</class>
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<class>edu.mit.broad.picard.util.IntervalTree</class>
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<class>edu.mit.broad.picard.util.OverlapDetector</class>
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<class>edu.mit.broad.picard.util.PasteParser</class>
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<class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
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<class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
|
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<class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
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<class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
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<class>edu.mit.broad.picard.variation.VariantType</class>
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<class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
|
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<class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
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<class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
|
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<class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
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<class>edu.mit.broad.picard.variation.KnownVariant</class>
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<class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
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<class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
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</dependencies>
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</executable>
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</package>
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@ -1,9 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>SomaticCoverage</name>
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<main-class>org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool</main-class>
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<dependencies>
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<class>org.broadinstitute.sting.playground.gatk.walkers.SomaticCoverageWalker</class>
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<file>java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml</file>
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</dependencies>
|
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</package>
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@ -1,5 +1,8 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
|
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<name>VCFValidator</name>
|
||||
<main-class>org.broadinstitute.sting.utils.genotype.vcf.VCFValidator</main-class>
|
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<executable>
|
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<name>VCFValidator</name>
|
||||
<main-class>org.broadinstitute.sting.utils.genotype.vcf.VCFValidator</main-class>
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</executable>
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</package>
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