kshakir 8855f080c2 For the fullCallingPipeline.q: ... - 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		2011-01-20 22:34:43 +00:00
..
TraverseTest.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
TraverseTestProf.sh	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
getFirehosePipelineYaml.sh	Now populating the refseq and dbsnp in awk instead of retrieving from firehose.	2011-01-19 18:19:10 +00:00
pipelineJobs.csh	watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress	2011-01-09 13:09:30 +00:00
queue.sh	For the fullCallingPipeline.q:	2011-01-20 22:34:43 +00:00
queueStatus.csh	Better queue status messages	2010-12-22 20:17:28 +00:00
runGATKReport.csh	no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size	2011-01-02 13:27:37 +00:00
runbeagle.sh	a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.	2010-07-06 18:33:28 +00:00
syncWithDevOnGSA2.csh	Deleting old shell code	2011-01-07 21:36:16 +00:00