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7 Commits (32fc221ffe631fcd040fefd5df663b6fddd2d46c)

Author SHA1 Message Date
kshakir 32fc221ffe Replaced pattern matched pipeline spec with annotated objects. 
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
kshakir beb8a83ca4 Multiple inputs / outputs for rules. 
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
kshakir e96bcf2128 GSA-333 Replaced all accidental usages of getCanonicalPath (which should never be used) with getAbsolutePath. 
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
kshakir 0e3c76ab84 GSA-333 Meant to use getAbsolutePath and not deref symlinks. 
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
depristo 99aae4ac0b ended not done for LSF queue submission. 
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
kshakir ed4d8ddd05 Refactoring and sugar to give lower level access to the job graph. 
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
kshakir e9ee55d7dd A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 
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