Added a QFunction.jobLimitSeconds for experimentation, currently only used as the equivalent of bsub -W.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5002 348d0f76-0448-11de-a6fe-93d51630548a

scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala

@@ -63,6 +63,10 @@ class Lsf706JobRunner(function: CommandLineFunction) extends LsfJobRunner(functi
         request.options |= LibBat.SUB_JOB_NAME
       }
 
+      if (function.jobLimitSeconds.isDefined) {
+        request.rLimits(LibLsf.LSF_RLIMIT_RUN) = function.jobLimitSeconds.get
+      }
+
       writeExec()
       request.command = "sh " + exec
 

scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -37,6 +37,13 @@ trait QFunction extends Logging {
   /** Order the function was added to the graph. */
   var addOrder: List[Int] = Nil
 
+  /**
+   * EXPERIMENTAL AND NOT SUPPORTED!!
+   * Limits the number of seconds that the job will run.
+   * TODO: Replace with full resource specifications.
+   */
+  var jobLimitSeconds: Option[Int] = None
+
   /**
    * A callback for modifying the run.
    * NOTE: This function is for ADVANCED use only and is unsupported.