kshakir 24ef2be02d Updated firehose pulldown shell scripts: ... - a LOT more error reporting to stderr and exit codes - split the firehose pull down into a TSV generators and a TSV to YAML converter - YAML converter is compatible with the TSVs generated by the front end website and will grab only the appropriate columns - deprecated getFirehosePipelineYaml.sh mode with a single Sample_Set name which uses the Firehose test harness - new getFirehosePipelineYamle.sh mode using web services API and requires an additional parameter, a password config file with "-u <user>:<pass>" which has been tested on problematic Sample_Sets git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5313 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-25 00:23:05 +00:00
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firehose	Updated firehose pulldown shell scripts:	2011-02-25 00:23:05 +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
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	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00
queueStatus.csh	Better queue status messages	2010-12-22 20:17:28 +00:00
runGATKReport.csh	Forgot to enable printing	2011-02-19 14:51:33 +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	V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism	2011-01-24 16:45:07 +00:00