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Expose time between checks for whether new jobs can be submitted as a user-settable parameter on CLi. Useful when testing pipelines to make idle time shorter. Contributed by @dakl (Daniel Klevebring on GATK forum).

This commit is contained in:
Geraldine Van der Auwera 2016-01-21 14:40:58 -05:00
parent 76817fe5ec
commit a46a4a6175
2 changed files with 4 additions and 1 deletions
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2
public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala
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@ -542,7 +542,7 @@ class QGraph extends Logging {
lastRunningCheck > 0 && nextRunningCheck(lastRunningCheck) <= 0
private def nextRunningCheck(lastRunningCheck: Long) =
((30 * 1000L) - (System.currentTimeMillis - lastRunningCheck))
((this.settings.time_between_checks.toLong * 1000L) - (System.currentTimeMillis - lastRunningCheck))
def formattedStatusCounts: String = {
"%d Pend, %d Run, %d Fail, %d Done".format(

3
public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala
View File

@ -55,6 +55,9 @@ class QGraphSettings {
@Argument(fullName="retry_failed", shortName="retry", doc="Retry the specified number of times after a command fails. Defaults to no retries.", required=false)
var retries = 0
@Argument(fullName="time_between_checks", shortName="tbc", doc="Seconds between checks of whether new jobs can be run. Default 30.", required=false)
var time_between_checks = 30.0
@Argument(fullName="start_from_scratch", shortName="startFromScratch", doc="Runs all command line functions even if the outputs were previously output successfully.", required=false)
var startFromScratch = false