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Cleaning up obsolete code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5044 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-01-21 16:27:35 +00:00
parent 8d46cf3604
commit 6fbd18c759
5 changed files with 2 additions and 18 deletions
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3
scala/src/org/broadinstitute/sting/queue/QSettings.scala
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@ -29,9 +29,6 @@ class QSettings {
@Argument(fullName="temp_directory", shortName="tempDir", doc="Temp directory to pass to functions.", required=false) @Argument(fullName="temp_directory", shortName="tempDir", doc="Temp directory to pass to functions.", required=false)
var tempDirectory = new File(System.getProperty("java.io.tmpdir")) var tempDirectory = new File(System.getProperty("java.io.tmpdir"))
@Argument(fullName="mount_directory", shortName="mountDir", doc="Extra directory to automount via 'cd <dir>' before running functions.", required=false)
var mountDirectories: Set[File] = Set.empty[File]
@ArgumentCollection @ArgumentCollection
val emailSettings = new EmailSettings val emailSettings = new EmailSettings
} }

2
scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
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@ -29,7 +29,7 @@ trait CommandLineJobRunner extends JobRunner[CommandLineFunction] with Logging {
protected def writeExec() { protected def writeExec() {
var exec = new StringBuilder var exec = new StringBuilder
var dirs = function.mountDirectories var dirs = Set.empty[File]
for (dir <- function.jobDirectories) for (dir <- function.jobDirectories)
dirs += IOUtils.dirLevel(dir, 2) dirs += IOUtils.dirLevel(dir, 2)
if (dirs.size > 0) { if (dirs.size > 0) {

5
scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
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@ -34,9 +34,6 @@ trait QFunction extends Logging {
/** Temporary directory to write any files */ /** Temporary directory to write any files */
var jobTempDir: File = null var jobTempDir: File = null
/** Directories to mount via 'cd <dir>' before running the command. */
var mountDirectories: Set[File] = Set.empty[File]
/** Order the function was added to the graph. */ /** Order the function was added to the graph. */
var addOrder: List[Int] = Nil var addOrder: List[Int] = Nil
@ -308,8 +305,6 @@ trait QFunction extends Logging {
// Do not set the temp dir relative to the command directory // Do not set the temp dir relative to the command directory
jobTempDir = IOUtils.absolute(jobTempDir) jobTempDir = IOUtils.absolute(jobTempDir)
mountDirectories ++= qSettings.mountDirectories
absoluteCommandDirectory() absoluteCommandDirectory()
} }

8
scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
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@ -14,9 +14,6 @@ class FullCallingPipelineTest extends BaseTest {
private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/" private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
// Explicit directories known to cause problems due to automount failures, and not detected by @Input / @Outputs
private final val mountDirectories = Set("/broad/software")
// In fullCallingPipeline.q VariantEval is always compared against 129. // In fullCallingPipeline.q VariantEval is always compared against 129.
// Until the newvarianteval is finalized which will allow java import of the prior results, // Until the newvarianteval is finalized which will allow java import of the prior results,
// we re-run VariantEval to validate the run, and replicate that behavior here. // we re-run VariantEval to validate the run, and replicate that behavior here.
@ -111,11 +108,6 @@ class FullCallingPipelineTest extends BaseTest {
if (dataset.jobQueue != null) if (dataset.jobQueue != null)
pipelineCommand += " -jobQueue " + dataset.jobQueue pipelineCommand += " -jobQueue " + dataset.jobQueue
//for (dir <- mountDirectories)
// pipelineCommand += " -mountDir " + dir
if (PipelineTest.run)
System.getenv.foreach{case (name, value) => println("DEBUG_ENVIRONMENT: %s=%s".format(name, value))}
// Run the test, at least checking if the command compiles // Run the test, at least checking if the command compiles
PipelineTest.executeTest(testName, pipelineCommand, null) PipelineTest.executeTest(testName, pipelineCommand, null)

2
shell/queue.sh
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@ -14,4 +14,4 @@ use R-2.10
use Oracle-full-client use Oracle-full-client
use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1 use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -mountDir /broad/software -log queue_log.txt -statusTo corin -bsub $2 java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2