Commit 3ae49381 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Set remote command for local execution

parent dd6dc7b7
......@@ -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.broadinstitute.gatk.utils.runtime.ProcessSettings
import org.ggf.drmaa.JobTemplate
import scala.collection.mutable
......@@ -60,6 +61,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
case jt: JobTemplate => jt.setRemoteCommand(remoteCommand)
case ps: ProcessSettings => ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
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