kshakir 8ba3a5a43f Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs. ... GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines. When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly. Added the most basic of all example QScripts for debugging, Hello World. Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-10 21:07:29 +00:00
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ExampleCountReads.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
ExampleCustomWalker.scala	Allowing the Queue to run the GATK via -cp instead of only from -jar.	2010-08-27 16:25:59 +00:00
ExampleUnifiedGenotyper.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
HelloWorld.scala	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00