gatk-3.8/public/scala/src/org/broadinstitute/sting/queue/engine
Mark DePristo 0cc5c3d799 General improvements to Queue
-- Support for collecting resources info from DRMAA runners
-- Disabled the non-standard mem_free argument so that we can actually use our own SGE cluster gsa4
-- NCoresRequest is a testing queue script for this.
-- Added two command line arguments:
  -- multiCoreJerk: don't request multiple cores for jobs with nt > 1.  This was the old behavior but it's really not the best way to run parallel jobs.  Now with queue if you run nt = 4 the system requests 4 cores on your host.  If this flag is thrown, though, it will only request 1 and you'll just use 4, like a jerk
  -- job_parallel_env: parallel environment named used with SGE to request multicore jobs.  Equivalent to -pe job_parallel_env NT for NT > 1 jobs
2011-12-20 14:05:09 -05:00
..
drmaa General improvements to Queue 2011-12-20 14:05:09 -05:00
gridengine General improvements to Queue 2011-12-20 14:05:09 -05:00
lsf General improvements to Queue 2011-12-20 14:05:09 -05:00
shell Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
CommandLineJobManager.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
CommandLineJobRunner.scala Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
CommandLinePluginManager.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
FunctionEdge.scala Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
InProcessJobManager.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
InProcessRunner.scala Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
JobManager.scala Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline: 2011-08-22 15:13:27 -04:00
JobRunInfo.scala Now captures the exechost in the job report 2011-08-28 12:05:56 -04:00
JobRunner.scala JobRunInfo improvements 2011-08-23 17:11:22 -04:00
MappingEdge.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QEdge.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QGraph.scala Swapping Thread.sleep(0) with Object.wait(0) caused Queue to lock up. Thanks to rpoplin for pointing it out. 2011-10-28 15:51:03 -04:00
QGraphSettings.scala No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
QNode.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
RunnerStatus.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00