kshakir ca5db821ce Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality. ... Queue now submits new LSF jobs only after previous functions have completed successfully. When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs. Ported commands like creating directories and scatter/gather interval list to scala functions. Updates to LSF status tracking by porting the python to internally generated bash scripts. Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option? Changed BaseTest to allow scala to access paths to references. Changed the extension generator to default the analysis name to the walker "name". git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-06 18:29:56 +00:00
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org/broadinstitute/sting/queue	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
BaseTransitionTableCalculator.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
HelloWorld.scala	support for scala walkers	2009-08-28 00:15:01 +00:00
ScalaCountLoci.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00