Commit db4dcbca authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style changes

parent 66f1b6ec
......@@ -26,7 +26,6 @@ import org.ggf.drmaa.JobTemplate
import scala.collection.mutable
import scala.io.Source
import scala.sys.process.{ Process, ProcessLogger }
import scala.util.matching.Regex
import scala.collection.JavaConversions._
/** Biopet command line trait to auto check executable and cluster values */
......@@ -50,20 +49,18 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
val writer = new PrintWriter(file)
writer.println("set -eubf")
writer.println("set -o pipefail")
lines.foreach(writer.println(_))
lines.foreach(writer.println)
writer.close()
}
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
case jt: JobTemplate => {
case jt: JobTemplate =>
changeScript(new File(jt.getArgs.head.toString))
jt.setRemoteCommand(remoteCommand)
}
case ps: ProcessSettings => {
case ps: ProcessSettings =>
changeScript(new File(ps.getCommand.tail.head))
ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
}
}
/**
......@@ -135,10 +132,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
that.beforeGraph()
that.internalBeforeGraph()
this match {
case p: BiopetPipe => {
case p: BiopetPipe =>
p.commands.last._outputAsStdout = true
new BiopetPipe(p.commands ::: that :: Nil)
}
case _ => new BiopetPipe(List(this, that))
}
}
......@@ -209,7 +205,6 @@ object BiopetCommandLineFunction extends Logging {
if (executable != null) {
if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
try {
val oldExecutable = executable
val buffer = new StringBuffer()
val cmd = Seq("which", executable)
val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
......
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