Setting the walltime

Signed-off-by: Joel Thibault <thibault@broadinstitute.org>

public/scala/src/org/broadinstitute/sting/queue/QSettings.scala

@@ -31,6 +31,10 @@ import org.broadinstitute.sting.commandline.{ClassType, Argument}
  * Default settings settable on the command line and passed to CommandLineFunctions.
  */
 class QSettings {
+  
+  @Argument(fullName="job_walltime", shortName="wallTime", doc="Setting the required walltime when using the drmaa job runner.", required=false)
+  var jobWalltime: Option[Long] = None
+  
   @Argument(fullName="run_name", shortName="runName", doc="A name for this run used for various status messages.", required=false)
   var runName: String = _
 

public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala

@@ -65,6 +65,9 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
         drmaaJob.setJoinFiles(true)
       }
 
+      if(function.wallTime != null)
+    	  drmaaJob.setHardWallclockTimeLimit(function.wallTime.get)      
+      
       drmaaJob.setNativeSpecification(functionNativeSpec)
 
       // Instead of running the function.commandLine, run "sh <jobScript>"

public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -33,6 +33,9 @@ import org.broadinstitute.sting.commandline.Argument
 trait CommandLineFunction extends QFunction with Logging {
   def commandLine: String
 
+  /** Setting the wall time request for drmaa job*/
+  var wallTime: Option[Long] = None
+  
   /** Upper memory limit */
   @Argument(doc="Memory limit", required=false)
   var memoryLimit: Option[Double] = None
@@ -67,6 +70,9 @@ trait CommandLineFunction extends QFunction with Logging {
     super.copySettingsTo(function)
     function match {
       case commandLineFunction: CommandLineFunction =>
+        if(commandLineFunction.wallTime.isEmpty)
+          commandLineFunction.wallTime = this.wallTime
+        
         if (commandLineFunction.memoryLimit.isEmpty)
           commandLineFunction.memoryLimit = this.memoryLimit
 
@@ -110,6 +116,10 @@ trait CommandLineFunction extends QFunction with Logging {
    * Sets all field values.
    */
   override def freezeFieldValues() {
+   
+    if(wallTime.isEmpty)
+      wallTime = qSettings.jobWalltime
+    
     if (jobQueue == null)
       jobQueue = qSettings.jobQueue