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gatk-3.8/scala/src/org/broadinstitute/sting/queue/engine
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kshakir 56433ebf6b Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 
- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-10 04:36:06 +00:00
..
DispatchJobRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
FunctionEdge.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
InProcessJobManager.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
InProcessRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
JobManager.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
JobRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
Lsf706JobManager.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
Lsf706JobRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
LsfJobRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
MappingEdge.scala 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
QEdge.scala 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
QGraph.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
QGraphSettings.scala Queue UI Improvements: 2010-10-26 19:49:08 +00:00
QNode.scala Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +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
ShellJobManager.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
ShellJobRunner.scala Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00