(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 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
removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 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
- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a
Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output. This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
Modified build script so that queue is cleaned during "ant clean".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
Will add more sugar / glue depending on how much of a graph the python generator outputs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3435 348d0f76-0448-11de-a6fe-93d51630548a
Current version only has syntatic sugar for accessing the graph via rules ex. "bam" -> "bam.bai", "samtools index ${bam}" and DOES NOT have sugar for constructing your own graph.
Usage info on the internal wiki at https://iwww.broadinstitute.org/gsa/wiki/index.php/Queue
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3420 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
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