Working on adding CGHub query
moving xml directory
Working on adding cghub into the map
Working on decider
Bugs
Working on map to include cghub
Updated decider
Working on the decider
Updates
Switching to "local" workflow mode as the default for the testing mode
props
Updating the help message
updating to create links dir
Working on 2.5 increment
Added some comments that contain examples for synapse
Upped the memory requiremnts for workflow.  Updated decider ini
only delete input file if using gtdownload
Small mem jobs are now 3G instead of 2 which caused Java out of memory issues on some system (but not all which is annoying). Try tuning for your cluster.
Fixed wrong bam input path
merged from brian_workflow_2.5 branched. Fixed the conflict by overwriting edit to the workflow_decider.pl on the develop using brians branch