As of October 17th 2013, Ludei has added Ouya Controller to CocoonJS Version 1.4.4. If you don't know what CocoonJS is, then I recommend you visit the link below. This tutorial will assume that you know how to export/submit your games through CocoonJS. Now there's an option to export to Ouya apk when you submit your game through Ludei's CocoonJS.
https://www.google.com/url?q=https://www.scirra.com/tutorials/303/how-to-export-to-cocoonjs&sa=U&ei=uW9fUvmTK62-4APcq4CgBw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNE0eZ1AtEibtQXljRZSv6_rr6Af0Q