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biopet.biopet
Commits
41857e5d
Commit
41857e5d
authored
Sep 27, 2015
by
Peter van 't Hof
Browse files
Overrider default shell from queue
parent
5096c156
Changes
1
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
41857e5d
...
...
@@ -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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