From ef50e77ee2ca761bedee7f27c97213e5c4246374 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Tue, 10 Jan 2012 16:10:25 -0500 Subject: [PATCH] When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified. Updated VE strats in the HSP for plotting Ka/Ks by AC. --- .../sting/queue/engine/shell/ShellJobRunner.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala index 5232dd4ea..5cac9ecf9 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * Copyright (c) 2012, The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.runtime.{ProcessSettings, OutputStreamSett /** * Runs jobs one at a time locally + * @param function Command to run. */ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner { // Controller on the thread that started the job @@ -39,13 +40,12 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu /** * Runs the function on the local shell. - * @param function Command to run. */ def start() { val commandLine = Array("sh", jobScript.getAbsolutePath) val stdoutSettings = new OutputStreamSettings val stderrSettings = new OutputStreamSettings - val mergeError = (function.jobErrorFile != null) + val mergeError = (function.jobErrorFile == null) stdoutSettings.setOutputFile(function.jobOutputFile, true) if (function.jobErrorFile != null)