Commit 41857e5d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Overrider default shell from queue

parent 5096c156
......@@ -22,6 +22,7 @@ import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.ggf.drmaa.JobTemplate
import scala.collection.mutable
import scala.sys.process.{ Process, ProcessLogger }
......@@ -52,6 +53,15 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
var executable: String = _
/** This is the default shell for drmaa jobs */
def defaultRemoteCommand = "bash"
private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
case jt:JobTemplate => jt.setRemoteCommand(remoteCommand)
}
/**
* Can override this method. This is executed just before the job is ready to run.
* Can check on run time files from pipeline here
......
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