Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
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
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
- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
Changed the FCP.q to use an InProcessFunction work around the -runDir issue GSA-420.
Tested the FCPTest using the following dotkits and "ant clean pipelinetest -Dpipeline.run=run":
- R-2.11
- Oracle-full-client
- .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
R-2.10,
Oracle-full-client,
cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
This also removes the unused titv argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5024 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
corin
chartl