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biopet.biopet
Commits
3ae49381
Commit
3ae49381
authored
Sep 28, 2015
by
Peter van 't Hof
Browse files
Set remote command for local execution
parent
dd6dc7b7
Changes
1
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
3ae49381
...
...
@@ -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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