Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
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
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
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
Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
kshakir