Added gene ordering tool for the synmap workflow.
Added python 3 fixes and makeflow fixes.

* Bytes passed in python 3 are now properly converted to ascii.
* Unicode strings are now sent using the zmq library.
* Jobs will not include there commands to be sent with makeflow.
  - This enforces that the correct commands are installed at the
    specified path.
* Makeflow should not report running until a makeflow log exists.