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One less Queue command line requirement: -tempDir now defaults to .queue/tmp. 

Also moved queueScatterGather to .queue/scatterGather.
This commit is contained in:
Khalid Shakir 2012-08-27 12:04:50 -04:00
parent 68c5142d2d
commit 2d1ea7124b
3 changed files with 19 additions and 8 deletions
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17
public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
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@ -48,14 +48,23 @@ public class IOUtils {
* @param tempDir Temporary directory. * @param tempDir Temporary directory.
*/ */
public static void checkTempDir(File tempDir) { 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(); String tempDirPath = tempDir.getAbsolutePath();
// Keeps the user from leaving the temp directory as the default, and on Macs from having pluses // 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. // 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/ // 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/"))) return (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());
} }
/** /**

8
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
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@ -64,10 +64,10 @@ object QCommandLine extends Logging {
Runtime.getRuntime.removeShutdownHook(shutdownHook) Runtime.getRuntime.removeShutdownHook(shutdownHook)
qCommandLine.shutdown() qCommandLine.shutdown()
} catch { } 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) if (CommandLineProgram.result != 0)
System.exit(CommandLineProgram.result); System.exit(CommandLineProgram.result)
} catch { } catch {
case e: Exception => CommandLineProgram.exitSystemWithError(e) case e: Exception => CommandLineProgram.exitSystemWithError(e)
} }
@ -105,9 +105,11 @@ class QCommandLine extends CommandLineProgram with Logging {
def execute = { def execute = {
if (settings.qSettings.runName == null) if (settings.qSettings.runName == null)
settings.qSettings.runName = FilenameUtils.removeExtension(scripts.head.getName) 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) qGraph.initializeWithSettings(settings)
val allQScripts = pluginManager.createAllTypes(); val allQScripts = pluginManager.createAllTypes()
for (script <- allQScripts) { for (script <- allQScripts) {
logger.info("Scripting " + pluginManager.getName(script.getClass.asSubclass(classOf[QScript]))) logger.info("Scripting " + pluginManager.getName(script.getClass.asSubclass(classOf[QScript])))
loadArgumentsIntoObject(script) loadArgumentsIntoObject(script)

2
public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
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@ -91,7 +91,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
if (qSettings.jobScatterGatherDirectory != null) { if (qSettings.jobScatterGatherDirectory != null) {
this.scatterGatherDirectory = IOUtils.absolute(qSettings.jobScatterGatherDirectory) this.scatterGatherDirectory = IOUtils.absolute(qSettings.jobScatterGatherDirectory)
} else { } else {
this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, "queueScatterGather") this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, ".queue/scatterGather")
} }
} }
} }