Mark DePristo 9eec33ec3b Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running ... -- Queue will incrementally now write out its jobReport.txt file whenever jobs finish running (FAIL or DONE) -- This makes it far easier to track what's going on, or to analyze incrementally performance results coming out of Queue -- Generally cleaned up the QJobsReporting code, creating a new clean class QJobsReporter that holds all of the information on what to do log and where to put into, which was previously scattered in QCommandLine and QJobReport		2012-08-21 14:44:18 -04:00
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drmaa	General improvements to Queue	2011-12-20 14:05:09 -05:00
gridengine	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00
lsf	Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts	2012-08-17 11:49:01 -04:00
shell	When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified.	2012-01-10 16:10:25 -05:00
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	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00
InProcessJobManager.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
InProcessRunner.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
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	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00
JobRunner.scala	JobRunInfo improvements	2011-08-23 17:11:22 -04:00
MappingEdge.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
QEdge.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
QGraph.scala	Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running	2012-08-21 14:44:18 -04:00
QGraphSettings.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
QNode.scala	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
RunnerStatus.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00