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
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engine	General improvements to Queue	2011-12-20 14:05:09 -05:00
extensions	Queue now properly escapes all shell arguments in generated shell scripts	2011-12-01 18:13:44 -05:00
function	General improvements to Queue	2011-12-20 14:05:09 -05:00
library	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.	2011-11-17 13:56:42 -05:00
util	Support for NT testing (default up to 4) for CC and UG	2011-12-14 18:45:00 -05:00
QCommandLine.scala	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	Now captures the exechost in the job report	2011-08-28 12:05:56 -04:00
QScriptManager.scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
QSettings.scala	General improvements to Queue	2011-12-20 14:05:09 -05:00