kshakir 2ec3852acd Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass. ... Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass. QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]]. Added an QCommandPlugin.initScript utility method for handling specialized script types.		2012-11-04 23:55:12 -05:00
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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	Fixed package error and a few deprecated scala warnings.	2012-10-15 15:29:40 -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	Sending a version of per job status messages.	2012-10-23 15:55:47 -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
QStatusMessenger.scala	Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.	2012-11-04 23:55:12 -05:00
RunnerStatus.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00