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
735ef19dc8
Added option to sleep after creating temporary directories.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3900 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:53:17 +00:00
82c37fceb5
Create intermediate directories and don't error if the directory already exists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3899 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:45:12 +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
f35e6d73b4
Actually name the class the name of the file. (Clearly created by cp)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3892 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-28 15:18:04 +00:00
cd9395fa14
Since Picard's FixMateInformation merges, fixes mates, and sorts, allow it to be used as a gather function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3891 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-28 15:09:19 +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
6bf5df4eb5
Better merge command
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3797 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-15 17:02:47 +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
a46e22ed13
Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3689 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 18:55:57 +00:00
178cf64a0c
Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3688 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 18:37:58 +00:00
dce2c17404
Added "-bsubWait" where Queue waits for all the jobs to exit before exiting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3661 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 19:52:17 +00:00
c047232b18
Using picard for bam merging.
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Properties now propagate to scatter/gather functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3659 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 17:59:09 +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
ce27ed0d60
Added missing @ClassType to memory limits.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3641 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 18:56:35 +00:00
30cf78fdc0
Refactoring for a first version of scatter gather api with basic shell script implementations.
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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
2010-06-22 18:39:20 +00:00
c44fd05aa1
Fix for a reflection issue with generic types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3565 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:58:38 +00:00
32fc221ffe
Replaced pattern matched pipeline spec with annotated objects.
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Old version is no longer available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 04:43:46 +00:00
beb8a83ca4
Multiple inputs / outputs for rules.
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Cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3464 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-30 08:28:16 +00:00
e96bcf2128
GSA-333 Replaced all accidental usages of getCanonicalPath (which should never be used) with getAbsolutePath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3463 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 22:27:05 +00:00
0e3c76ab84
GSA-333 Meant to use getAbsolutePath and not deref symlinks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3449 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 21:23:02 +00:00
99aae4ac0b
ended not done for LSF queue submission.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3446 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 22:16:48 +00:00
ed4d8ddd05
Refactoring and sugar to give lower level access to the job graph.
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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
2010-05-25 22:52:29 +00:00
e9ee55d7dd
A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps.
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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
2010-05-23 20:21:09 +00:00
chartl
kshakir
depristo