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Defaulting the MFCP to run without a tear script. 

Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done.
Enabled the MCFPTest for the first time, running without the tear script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-02-17 21:13:14 +00:00
parent 49931b12fb
commit 860b172ef1
2 changed files with 13 additions and 6 deletions
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17
scala/qscript/playground/MultiFullCallingPipeline.scala
View File

@ -28,13 +28,16 @@ class MultiFullCallingPipeline extends QScript {
@Argument(doc="pipeline priority", shortName="PP", required = false) @Argument(doc="pipeline priority", shortName="PP", required = false)
var pipelinePriority: Option[Int] = None var pipelinePriority: Option[Int] = None
@Argument(doc="run with -tearScript", shortName="TS")
var runWithTearScript = false
def script { def script {
// Global arguments for all pipeline runs // Global arguments for all pipeline runs
stingHome = IOUtils.absolute(stingHome) stingHome = IOUtils.absolute(stingHome)
val queueJar = new File(stingHome, "dist/Queue.jar") val queueJar = new File(stingHome, "dist/Queue.jar")
val pipelineScript = new File(stingHome, "scala/qscript/playground/FullCallingPipeline.q") val pipelineScript = new File(stingHome, "scala/qscript/playground/FullCallingPipeline.q")
val gatkJar = new File(stingHome, "dist/GenomeAnalysisTK.jar") val gatkJar = new File(stingHome, "dist/GenomeAnalysisTK.jar")
val tearScript = new File(stingHome, "R/DataProcessingReport/GetTearsheetStats.R") val tearScript = if (runWithTearScript) new File(stingHome, "R/DataProcessingReport/GetTearsheetStats.R") else null
// Parse the yaml list // Parse the yaml list
var yamls = List.empty[File] var yamls = List.empty[File]
@ -64,23 +67,27 @@ class MultiFullCallingPipeline extends QScript {
* run has produced the passed in output file. * run has produced the passed in output file.
*/ */
class RunPipeline(yamlFile: File, lastOutput: File) extends JarCommandLineFunction { class RunPipeline(yamlFile: File, lastOutput: File) extends JarCommandLineFunction {
private var yamlName = yamlFile.getName.stripSuffix(".yaml")
@Input(doc="output file to wait for", required=false) @Input(doc="output file to wait for", required=false)
var waitJobOutputFile = lastOutput var waitJobOutputFile = lastOutput
@Output(doc="virtual output file tagging this pipeline as complete")
var pipelineComplete = new File(yamlFile.getParentFile, yamlName + ".mfcp")
commandDirectory = yamlFile.getParentFile commandDirectory = yamlFile.getParentFile
jobOutputFile = IOUtils.absolute(commandDirectory, "queue.out") jobOutputFile = IOUtils.absolute(commandDirectory, "queue.out")
jarFile = queueJar jarFile = queueJar
memoryLimit = Some(1) memoryLimit = Some(1)
private var yamlName = yamlFile.getName.stripSuffix(".yaml")
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
optional(" -statusTo ", qscript.pipelineStatusTo) + optional(" -statusTo ", qscript.pipelineStatusTo) +
optional(" -jobQueue ", qscript.pipelineJobQueue) + optional(" -jobQueue ", qscript.pipelineJobQueue) +
optional(" -shortJobQueue ", qscript.pipelineShortQueue) + optional(" -shortJobQueue ", qscript.pipelineShortQueue) +
optional(" -jobPriority ", qscript.pipelinePriority) + optional(" -jobPriority ", qscript.pipelinePriority) +
" -S %s --gatkjar %s -tearScript %s -jobProject %s -jobPrefix %s -Y %s -bsub -run" optional(" -tearScript ", tearScript) +
.format(pipelineScript, gatkJar, tearScript, yamlName, yamlName, yamlFile) " -S %s --gatkjar %s -jobProject %s -jobPrefix %s -Y %s -bsub -run"
.format(pipelineScript, gatkJar, yamlName, yamlName, yamlFile)
override def dotString = "Queue: " + yamlName override def dotString = "Queue: " + yamlName
} }

2
scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
View File

@ -54,7 +54,7 @@ class MultiFullCallingPipelineTest {
final def convertDatasets: Array[Array[AnyRef]] = final def convertDatasets: Array[Array[AnyRef]] =
datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
@Test(dataProvider="datasets", enabled=false) @Test(dataProvider="datasets")
def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) = { def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) = {
val projectName = dataset.name val projectName = dataset.name
val testName = "MultiFullCallingPipeline-" + projectName val testName = "MultiFullCallingPipeline-" + projectName