kshakir 2058fc12bc Small bug fixes: ... Added a property to allow generating Queue extensions around an external version of the GATK. Updated argument order in -help. Restored the ability to use QScript trait imported annotations in constructors. Removing line feeds from email password files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5416 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-10 19:54:14 +00:00
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gridengine	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
lsf	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
shell	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
CommandLineJobManager.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
CommandLineJobRunner.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
CommandLinePluginManager.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
FunctionEdge.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
InProcessJobManager.scala	Moved some shutdown logic from the LSF job runner into the QGraph.	2011-01-25 20:28:54 +00:00
InProcessRunner.scala	Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests.	2011-01-25 04:11:49 +00:00
JobManager.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
JobRunner.scala	JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706.	2011-03-07 23:52:48 +00:00
MappingEdge.scala	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
QEdge.scala	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
QGraph.scala	Printing out counts of functions as they are dispatched.	2011-03-10 01:45:20 +00:00
QGraphSettings.scala	Small bug fixes:	2011-03-10 19:54:14 +00:00
QNode.scala	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
RunnerStatus.scala	QScript authors can now tag functions as intermediate. Functions tagged as intermediate will be skipped unless another function in the graph needs their output.	2010-10-18 22:11:14 +00:00