DOT visualization with Queue. More sophisticated recalibation queue script with scatter/gather
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3799 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
ab84ed8c68
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81eef0d993
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@ -4,26 +4,30 @@ import org.apache.commons.io.FilenameUtils;
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val unusedArgs = setArgs(args)
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def runPipeline() = {
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def runPipeline(arg: String) = {
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val scatter = arg == "scatter"
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for (bamIn <- inputs(".bam")) {
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val root = bamIn.getPath()
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val bamRoot = FilenameUtils.removeExtension(root);
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val recalData = bamRoot + ".recal_data.csv"
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val recalBam = bamRoot + ".recal.bam"
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val recalRecalData = bamRoot + ".recal.recal_data.csv"
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val recalData = new File(bamRoot + ".recal_data.csv")
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val recalBam = new File(bamRoot + ".recal.bam")
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val recalRecalData = new File(bamRoot + ".recal.recal_data.csv")
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//add(new CountCovariates(root, recalData, "-OQ"))
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val tableRecal = new TableRecalibrate(root, recalData, recalBam)
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tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
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tableRecal.scatterCount = 25
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val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam, "-OQ")
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if ( scatter ) {
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tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
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tableRecal.scatterCount = 25
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}
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add(tableRecal)
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add(new Index(recalBam))
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add(new CountCovariates(recalBam, recalRecalData))
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add(new AnalyzeCovariates(recalData, recalData + ".analyzeCovariates"))
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add(new AnalyzeCovariates(recalRecalData, recalRecalData + ".analyzeCovariates"))
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add(new CountCovariates(recalBam, recalRecalData, "-nt 4"))
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add(new AnalyzeCovariates(recalData, new File(recalData.getPath() + ".analyzeCovariates")))
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add(new AnalyzeCovariates(recalRecalData, new File(recalRecalData.getPath() + ".analyzeCovariates")))
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}
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}
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runPipeline()
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runPipeline(unusedArgs(0))
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// Populate parameters passed in via -P
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setParams
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@ -31,30 +35,30 @@ setParams
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// Run the pipeline
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run
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class Index(bamIn: String) extends GatkFunction {
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class Index(bamIn: File) extends GatkFunction {
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@Input(doc="foo") var bam = bamIn
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memoryLimit = Some(1)
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def commandLine = "samtools index %s".format(bam)
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}
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class CountCovariates(bamIn: String, recalDataIn: String, args: String = "") extends GatkFunction {
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class CountCovariates(bamIn: File, recalDataIn: File, args: String = "") extends GatkFunction {
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@Input(doc="foo") var bam = bamIn
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@Output(doc="foo") var recalData = recalDataIn
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memoryLimit = Some(4)
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def commandLine = gatkCommandLine("CountCovariates") + args + " -l INFO -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I %s --max_reads_at_locus 20000 -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile %s".format(bam, recalData)
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}
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class TableRecalibrate(bamInArg: String, recalDataIn: String, bamOutArg: String) extends GatkFunction {
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class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File, args: String = "") extends GatkFunction {
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@Input(doc="foo") var bamIn = bamInArg
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@Input(doc="foo") var recalData = recalDataIn
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@Gather(classOf[BamGatherFunction])
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@Output(doc="foo") var bamOut = new File(bamOutArg)
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@Output(doc="foo") var bamOut = bamOutArg
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memoryLimit = Some(2)
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def commandLine = gatkCommandLine("TableRecalibration") + "-l INFO -I %s -recalFile %s -outputBam %s".format(bamIn, recalData, bamOut.getPath())
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def commandLine = gatkCommandLine("TableRecalibration") + args + " -l INFO -I %s -recalFile %s -outputBam %s".format(bamIn, recalData, bamOut) // bamOut.getPath())
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}
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class AnalyzeCovariates(recalDataIn: String, outputDir: String) extends GatkFunction {
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class AnalyzeCovariates(recalDataIn: File, outputDir: File) extends GatkFunction {
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@Input(doc="foo") var recalData = recalDataIn
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memoryLimit = Some(4)
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def commandLine = "java -Xmx4g -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/AnalyzeCovariates.jar -recalFile %s -outputDir %s -resources /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/ -ignoreQ 5".format(recalData, outputDir)
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}
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def commandLine = "java -Xmx4g -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/AnalyzeCovariates.jar -recalFile %s -outputDir %s -resources /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/ -ignoreQ 5 -Rscript /broad/tools/apps/R-2.6.0/bin/Rscript".format(recalData, outputDir)
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}
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@ -103,6 +103,7 @@ object QScript {
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qGraph.add(function)
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qGraph.fillIn
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qGraph.run
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qGraph.renderToDot(new File("queue.dot"))
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}
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}
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}
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@ -1,5 +1,6 @@
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package org.broadinstitute.sting.queue.engine
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import org.jgrapht.traverse.TopologicalOrderIterator
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import org.jgrapht.graph.SimpleDirectedGraph
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import scala.collection.JavaConversions
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import scala.collection.JavaConversions._
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@ -9,6 +10,9 @@ import org.broadinstitute.sting.queue.util.{CollectionUtils, Logging}
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import org.broadinstitute.sting.queue.QException
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import org.jgrapht.alg.CycleDetector
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import org.jgrapht.EdgeFactory
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import org.jgrapht.ext.DOTExporter
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import org.broadinstitute.sting.queue.function.DispatchFunction
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import org.broadinstitute.sting.queue.function.gatk.GatkFunction
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class QGraph extends Logging {
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var dryRun = true
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@ -146,4 +150,22 @@ class QGraph extends Logging {
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private def isOrphan(node: QNode) =
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(jobGraph.incomingEdgesOf(node).size + jobGraph.outgoingEdgesOf(node).size) == 0
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def renderToDot(file: java.io.File) = {
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val out = new java.io.FileWriter(file)
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// todo -- we need a nice way to visualize the key pieces of information about commands. Perhaps a
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// todo -- visualizeString() command, or something that shows inputs / outputs
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val ve = new org.jgrapht.ext.EdgeNameProvider[QFunction] {
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def getEdgeName( function: QFunction ) = function match {
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case f: DispatchFunction => f.jobName + " => " + f.commandLine
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case _ => ""
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}
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}
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//val iterator = new TopologicalOrderIterator(qGraph.jobGraph)
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(new DOTExporter(new org.jgrapht.ext.IntegerNameProvider[QNode](), null, ve)).export(out, jobGraph)
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out.close
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}
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}
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