From 2d1ea7124b576764137cad7ca3f458a71a8fd69b Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Mon, 27 Aug 2012 12:04:50 -0400
Subject: [PATCH] One less Queue command line requirement: -tempDir now
 defaults to .queue/tmp. Also moved queueScatterGather to
 .queue/scatterGather.

---
 .../broadinstitute/sting/utils/io/IOUtils.java  | 17 +++++++++++++----
 .../sting/queue/QCommandLine.scala              |  8 +++++---
 .../ScatterGatherableFunction.scala             |  2 +-
 3 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
index 160df0e51..b79211e74 100644
--- a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
@@ -48,14 +48,23 @@ public class IOUtils {
      * @param tempDir Temporary directory.
      */
     public static void checkTempDir(File tempDir) {
+        if (isDefaultTempDir(tempDir))
+            throw new UserException.BadTmpDir("java.io.tmpdir must be explicitly set");
+        if (!tempDir.exists() && !tempDir.mkdirs())
+            throw new UserException.BadTmpDir("Could not create directory: " + tempDir.getAbsolutePath());
+    }
+
+    /**
+     * Returns true if the directory is a default temporary directory.
+     * @param tempDir the directory to check.
+     * @return true if the directory is a default temporary directory.
+     */
+    public static boolean isDefaultTempDir(File tempDir) {
         String tempDirPath = tempDir.getAbsolutePath();
         // Keeps the user from leaving the temp directory as the default, and on Macs from having pluses
         // in the path which can cause problems with the Google Reflections library.
         // see also: http://benjchristensen.com/2009/09/22/mac-osx-10-6-java-java-io-tmpdir/
-        if (tempDirPath.startsWith("/var/folders/") || (tempDirPath.equals("/tmp")) || (tempDirPath.equals("/tmp/")))
-            throw new UserException.BadTmpDir("java.io.tmpdir must be explicitly set");
-        if (!tempDir.exists() && !tempDir.mkdirs())
-            throw new UserException.BadTmpDir("Could not create directory: " + tempDir.getAbsolutePath());
+        return (tempDirPath.startsWith("/var/folders/") || (tempDirPath.equals("/tmp")) || (tempDirPath.equals("/tmp/")));
     }
 
     /**
diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index 775847ba9..0d0fab9d1 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -64,10 +64,10 @@ object QCommandLine extends Logging {
         Runtime.getRuntime.removeShutdownHook(shutdownHook)
         qCommandLine.shutdown()
       } catch {
-        case _ => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
+        case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
       }
       if (CommandLineProgram.result != 0)
-        System.exit(CommandLineProgram.result);
+        System.exit(CommandLineProgram.result)
     } catch {
       case e: Exception => CommandLineProgram.exitSystemWithError(e)
     }
@@ -105,9 +105,11 @@ class QCommandLine extends CommandLineProgram with Logging {
   def execute = {
     if (settings.qSettings.runName == null)
       settings.qSettings.runName = FilenameUtils.removeExtension(scripts.head.getName)
+    if (IOUtils.isDefaultTempDir(settings.qSettings.tempDirectory))
+      settings.qSettings.tempDirectory = IOUtils.absolute(settings.qSettings.runDirectory, ".queue/tmp")
     qGraph.initializeWithSettings(settings)
 
-    val allQScripts = pluginManager.createAllTypes();
+    val allQScripts = pluginManager.createAllTypes()
     for (script <- allQScripts) {
       logger.info("Scripting " + pluginManager.getName(script.getClass.asSubclass(classOf[QScript])))
       loadArgumentsIntoObject(script)
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
index 4578f0e82..5dd7d4c79 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -91,7 +91,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       if (qSettings.jobScatterGatherDirectory != null) {
         this.scatterGatherDirectory = IOUtils.absolute(qSettings.jobScatterGatherDirectory)
       } else {
-        this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, "queueScatterGather")
+        this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, ".queue/scatterGather")
       }
     }
   }