Add new 'module' XML tag, that can import modules from supplementary files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
ba19afd529
commit
e1fba42fdb
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@ -0,0 +1,17 @@
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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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<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.QualityScoreCovariate</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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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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</dependencies>
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</executable>
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</package>
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@ -32,28 +32,12 @@
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<!-- Create an output directory for the package -->
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<mkdir dir="{$package.dir}"/>
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<xsl:for-each select="executable">
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<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
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<jar jarfile="{concat($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/properties">
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<fileset file="{$staging.dir}/{current()}" />
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</xsl:for-each>
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<xsl:for-each select="dependencies/file">
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<fileset file="{$staging.dir}/{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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<!-- Create the executable sections -->
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<xsl:apply-templates select="executable" />
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<!-- Add in other modules -->
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<xsl:for-each select="module">
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<xsl:apply-templates select="document(current())/package/executable" />
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</xsl:for-each>
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<!-- Include various script files -->
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@ -97,6 +81,39 @@
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<symlink link="{concat($target.dir,'/',$short.name)}" resource="{$full.path}" overwrite="true" />
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</xsl:template>
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<xsl:template match="executable">
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<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
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<jar jarfile="{concat($package.dir,name,'.jar')}">
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<classfileset dir="{$staging.dir}">
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<root classname="{main-class}"/>
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</classfileset>
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<xsl:for-each select="properties">
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<fileset file="{$staging.dir}/{current()}" />
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</xsl:for-each>
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<xsl:for-each select="module">
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<xsl:apply-templates select="document(current())/package/executable/dependencies" />
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</xsl:for-each>
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<xsl:apply-templates select="dependencies" />
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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:template>
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<xsl:template match="dependencies">
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<classfileset dir="{$staging.dir}">
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<xsl:for-each select="package">
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<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
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</xsl:for-each>
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<xsl:for-each select="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="file">
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<fileset file="{$staging.dir}/{current()}" />
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</xsl:for-each>
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</xsl:template>
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<!-- Determine the short name (filename w/o directory structure of the given filename -->
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<xsl:template name="get-short-name">
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<xsl:param name="string"/>
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@ -6,46 +6,21 @@
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<executable>
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<name>GATK-GSA-Pipeline</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<properties>StingText.properties</properties>
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<module>QualityScoresRecalibrationModule.xml</module>
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<module>LocalRealignmentAroundIndelsModule.xml</module>
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<module>UnifiedGenotyperModule.xml</module>
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<module>VariantFiltrationModule.xml</module>
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<module>VariantAnnotatorModule.xml</module>
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<dependencies>
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<!-- Text extracted from the javadocs -->
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<properties>StingText.properties</properties>
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<!-- Filters -->
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<package>org.broadinstitute.sting.gatk.filters</package>
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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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<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</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.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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<!-- From playground -->
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<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
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<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
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@ -7,9 +7,13 @@
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<executable>
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<name>GATK-Picard</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<properties>StingText.properties</properties>
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<module>QualityScoresRecalibrationModule.xml</module>
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<module>LocalRealignmentAroundIndelsModule.xml</module>
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<module>UnifiedGenotyperModule.xml</module>
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<module>VariantFiltrationModule.xml</module>
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<module>VariantAnnotatorModule.xml</module>
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<dependencies>
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<!-- Text extracted from the javadocs -->
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<properties>StingText.properties</properties>
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<!-- Filters -->
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<package>org.broadinstitute.sting.gatk.filters</package>
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<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
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@ -18,41 +22,12 @@
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</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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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</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.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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<resources>
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@ -4,9 +4,14 @@
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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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<properties>StingText.properties</properties>
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<module>QualityScoresRecalibrationModule.xml</module>
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<module>LocalRealignmentAroundIndelsModule.xml</module>
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<module>UnifiedGenotyperModule.xml</module>
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<module>VariantFiltrationModule.xml</module>
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<module>VariantAnnotatorModule.xml</module>
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<module>VCFValidatorModule.xml</module>
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<dependencies>
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<!-- Text extracted from the javadocs -->
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<properties>StingText.properties</properties>
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<!-- Filters -->
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<package>org.broadinstitute.sting.gatk.filters</package>
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<!-- Basic qc walkers -->
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@ -16,40 +21,6 @@
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</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.QualityScoreCovariate</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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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</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.QualByDepth</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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<!-- VCF validator -->
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<class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
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</dependencies>
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</executable>
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<executable>
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@ -0,0 +1,19 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>LocalRealignmentAroundIndels</name>
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<executable>
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<name>LocalRealignmentAroundIndels</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<dependencies>
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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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</dependencies>
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</executable>
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</package>
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@ -0,0 +1,19 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>QualityScoresRecalibration</name>
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<executable>
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<name>QualityScoresRecalibration</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<dependencies>
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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.QualityScoreCovariate</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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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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</dependencies>
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</executable>
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</package>
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@ -0,0 +1,12 @@
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<?xml version="1.0" encoding="UTF-8"?>
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||||
<package>
|
||||
<name>UnifiedGenotyper</name>
|
||||
<executable>
|
||||
<name>UnifiedGenotyper</name>
|
||||
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
|
||||
<dependencies>
|
||||
<!-- Unified genotyper -->
|
||||
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
|
||||
</dependencies>
|
||||
</executable>
|
||||
</package>
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<package>
|
||||
<name>VCFValidator</name>
|
||||
<executable>
|
||||
<name>VCFValidator</name>
|
||||
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
|
||||
<dependencies>
|
||||
<!-- VCF validator -->
|
||||
<class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
|
||||
</dependencies>
|
||||
</executable>
|
||||
</package>
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<package>
|
||||
<name>VariantAnnotator</name>
|
||||
<executable>
|
||||
<name>VariantAnnotator</name>
|
||||
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
|
||||
<dependencies>
|
||||
<!-- Variant annotator -->
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
|
||||
<!-- And the annotations -->
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
|
||||
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
|
||||
</dependencies>
|
||||
</executable>
|
||||
</package>
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<package>
|
||||
<name>VariantFiltration</name>
|
||||
<executable>
|
||||
<name>VariantFiltration</name>
|
||||
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
|
||||
<dependencies>
|
||||
<!-- Variant filtration -->
|
||||
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
|
||||
</dependencies>
|
||||
</executable>
|
||||
</package>
|
||||
Loading…
Reference in New Issue