From d768c6558da6fc238ef39d924cee0d35f3248c9a Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 28 Oct 2010 15:00:21 +0000
Subject: [PATCH] Now that the user is required to set the java temp directory,
 it is safer for the LsfJobRunner to write to the java temp directory instead
 of the command directory.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4593 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/queue/engine/LsfJobRunner.scala    | 6 +++---
 scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala
index 6dab7e210..130f3b22c 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala
@@ -166,7 +166,7 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
    * @return the file path to the pre-exec.
    */
   private def writeExec() = {
-    IOUtils.writeTempFile(function.commandLine, ".exec", "", function.commandDirectory)
+    IOUtils.writeTempFile(function.commandLine, ".exec", "")
   }
 
   /**
@@ -185,7 +185,7 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
     mountCommand(function).foreach(command =>
       preExec.append("%s%n".format(command)))
 
-    IOUtils.writeTempFile(preExec.toString, ".preExec", "", function.commandDirectory)
+    IOUtils.writeTempFile(preExec.toString, ".preExec", "")
   }
 
   /**
@@ -211,6 +211,6 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
   |fi
   |""".stripMargin.format(function.commandDirectory, touchDone, touchFail))
 
-    IOUtils.writeTempFile(postExec.toString, ".postExec", "", function.commandDirectory)
+    IOUtils.writeTempFile(postExec.toString, ".postExec", "")
   }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala b/scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala
index fcd8a3d0f..3e9df9c50 100644
--- a/scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala
+++ b/scala/src/org/broadinstitute/sting/queue/util/IOUtils.scala
@@ -89,7 +89,7 @@ object IOUtils {
 
   def writeContents(file: File, content: String) =  FileUtils.writeStringToFile(file, content)
 
-  def writeTempFile(content: String, prefix: String, suffix: String = "", directory: File) = {
+  def   writeTempFile(content: String, prefix: String, suffix: String = "", directory: File = null) = {
     val tempFile = absolute(File.createTempFile(prefix, suffix, directory))
     writeContents(tempFile, content)
     tempFile