cd2d051209
full path to Rscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3999 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:02:38 +00:00
9b432d0801
1kg script now works
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3998 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:01:18 +00:00
4f51a02dea
Changed logging level to default at INFO instead of WARN.
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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
2010-08-09 16:42:48 +00:00
5815348ebc
Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3941 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 20:05:27 +00:00
9132c98eec
Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 22:04:02 +00:00
54d93f63d2
Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 21:35:50 +00:00
0f9baa2e94
Ha ha ha ha ha
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:(
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:48:35 +00:00
7a5ee485d2
Full pipeline now works through DAG creation. First draft; more work to do to make it cleaner and better command-line input handling (and properties handling); but the DAG is rendered and looks good.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3898 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:36:17 +00:00
4d4cf6e1dc
Updates to calling pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:37:20 +00:00
62a9217a61
A brute-force exome/genome independent end-to-end cleaning/calling pipeline using Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3894 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 13:17:14 +00:00
25a27b78bc
1KG Table 1 counting pipeline. Useful example
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3819 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-17 22:30:56 +00:00
b0fc42906e
Better DOT support and updated recalibration pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3811 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 20:54:51 +00:00
81eef0d993
DOT visualization with Queue. More sophisticated recalibation queue script with scatter/gather
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3799 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-15 22:32:48 +00:00
530a320f28
Intermediate commit of scatter/gather recalibation pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3785 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-13 22:46:08 +00:00
1d399aa2f3
Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3757 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-11 03:27:32 +00:00
7be8c35eb2
Workaround for scala trait erasing parameterized types:
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- 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
2010-07-07 03:15:10 +00:00
87470d5fe5
Checking in a simplistic VR qscript file for posterity's sake
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3705 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 18:53:17 +00:00
894ad354fa
Fixed typo in the name of the shell directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3644 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 20:59:40 +00:00
75c98c42b8
Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.
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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
2010-06-25 20:51:13 +00:00
depristo
kshakir
chartl
rpoplin