Commit 02e65123 authored by Sander Bollen's avatar Sander Bollen
Browse files

jobtimelimit in core

parent 21452691
......@@ -58,6 +58,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
var jobDelayTime: Option[Int] = config("job_delay_time")
/**
* wall clock time limit in seconds for a job
*/
var jobWallClockTimeLimit: Option[Int] = config("job_wall_time_limit")
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
case jt: JobTemplate =>
......@@ -99,6 +104,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
_pipesJobs.foreach(_.beforeGraph())
_pipesJobs.foreach(_.internalBeforeGraph())
jobWallClockTimeLimit.foreach(x => jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$x"))
}
......
......@@ -128,9 +128,7 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
override def defaultCoreMemory = 50
// wallclock time limit in seconds
var wallClockTimeLimit: Int = config("wall_time_limit", namespace = "freec", default = 7200)
jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$wallClockTimeLimit")
jobWallClockTimeLimit = config("job_wall_time_limit", namespace = "freec", default = 7200)
private var configFile: File = _
......
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