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3 Commits (b1e4e1afb65fa1a208794c8d7d284c82efbd541a)

Author SHA1 Message Date
kshakir 4ee4fd47e9 Moved the test name and the job queue into the spec. 
Defaulting to the hour queue for running pipeline tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5122 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-29 00:07:25 +00:00
kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. 
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-28 23:33:58 +00:00
kshakir 9923e05e0a Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 
Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript. 
Moved duplicated error handling from JobRunners into the FunctionEdge.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-25 04:11:49 +00:00