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Back to using the LSF job name during dry runs since when the real job ids weren't available '-w(null)' wasn't too informative. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4107 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-08-25 15:18:02 +00:00
parent b4baa3eb8f
commit 4eff69d95e
1 changed files with 10 additions and 3 deletions
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13
scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala
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@ -46,7 +46,8 @@ class LsfJobRunner extends DispatchJobRunner with Logging {
} }
if (previous.size > 0) if (previous.size > 0)
job.extraBsubArgs ++= List("-w", dependencyExpression(previous, function.jobRunOnlyIfPreviousSucceed)) job.extraBsubArgs ++= List("-w", dependencyExpression(previous,
function.jobRunOnlyIfPreviousSucceed, qGraph.dryRun))
addJob(function, qGraph, job, previous) addJob(function, qGraph, job, previous)
@ -64,10 +65,16 @@ class LsfJobRunner extends DispatchJobRunner with Logging {
* Returns the dependency expression for the prior jobs. * Returns the dependency expression for the prior jobs.
* @param jobs Previous jobs this job is dependent on. * @param jobs Previous jobs this job is dependent on.
* @param runOnSuccess Run the job only if the previous jobs succeed. * @param runOnSuccess Run the job only if the previous jobs succeed.
* @param dryRun If the current run is a dry run.
* @return The dependency expression for the prior jobs. * @return The dependency expression for the prior jobs.
*/ */
private def dependencyExpression(jobs: Iterable[LsfJob], runOnSuccess: Boolean) = { private def dependencyExpression(jobs: Iterable[LsfJob],
val jobIds = jobs.toSet[LsfJob].map(_.bsubJobId) runOnSuccess: Boolean, dryRun: Boolean) = {
val jobIds = if (dryRun)
jobs.toSet[LsfJob].map("\"" + _.name + "\"")
else
jobs.toSet[LsfJob].map(_.bsubJobId)
if (runOnSuccess) if (runOnSuccess)
jobIds.mkString("done(", ") && done(", ")") jobIds.mkString("done(", ") && done(", ")")
else else