- Catching errors when LSF fails and retrying.
- When LSF retries fail, catching the error, marking the job as failed, and no longer bkilling everything by exiting Queue.
- Caching function fields by class instead of each instance of a function saving a list of its fields.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4490 348d0f76-0448-11de-a6fe-93d51630548a
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
Removed extra quotes from 'cd' pre-exec command.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4067 348d0f76-0448-11de-a6fe-93d51630548a
-l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run.
More documentation in the examples with a new even simpler CountReads example.
Took out unused option to build Queue GATK extensions separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4025 348d0f76-0448-11de-a6fe-93d51630548a
Added ability to skip up-to-date jobs where the outputs are older than the inputs.
Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names.
Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile
Moved Hidden from the GATK to StingUtils.
Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7
Added Queue to javadoc and testing build targets.
Added first Queue unit test.
Another pass at avoiding cycles in the DAG thanks to all function I/O being files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4017 348d0f76-0448-11de-a6fe-93d51630548a
Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
kshakir