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
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examples	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +00:00
playground	For the fullCallingPipeline.q:	2011-01-20 22:34:43 +00:00