Merge pull request #1 from LyonsLab/evan-dev

Evan dev
Fixed bug in gene_order tool.

The tool would incorrectly check the wrong key in the dictionary
and repeatedly overwrite the dictionary entry at the top level.
ff-only
Added more logging and changed makeflow arguments.
Workflows that die will now be restarted.
Removed a previous change left.
Updated makeflow options.
Fixed parameters.
Cleaned up makeflow execution.
Added support to restart a workflow.
Added restarting a workflow.
Updated scheduling to fifo scheduling.
Fixed ordering of command arguments.
Added stop method to Service.
Major change to switching to work_queue.
Added package support.
Workqueue now properly schedules workflows.
Added input and output file checking.
Improved output logging format.
Code cleanup.