Lee; Thanks for all the patience with this. I'll take the errors in order:
Original exception was: Traceback (most recent call last): [...] raise TypeError("upgrade/downgrade functions must accept engine" TypeError: upgrade/downgrade functions must accept engine parameter (since version 0.5.4)
This was a typo in the downgrade function for one of the patches. I pushed a fix so if you update from bitbucket things should work smoothly again (once we get to problem 2 below). For anyone with galaxy-dist commit privileges, here's the one liner: https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf17731...
Thank you. I feel like this next error might be my fault (I don't know python very well). I think it is saying that I don't have a module, but it is installed via Ubuntu aptitude, so now I don't really know what to do next. I reinstalled the module like so: aptitude reinstall python-apport
$ sh manage_db.sh downgrade --version=108 112 -> 111... Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 64, in apport_excepthook from apport.fileutils import likely_packaged, get_recent_crashes ImportError: No module named apport.fileutils
The second error is complaining about this Ubuntu specific program after the initial error, so not sure what exactly happened here. It looks like there is a problem with this in Ubuntu 13.04: https://bugs.launchpad.net/ubuntu/+source/apport/+bug/1170479 Since this is an error report on top of your error report, I think it'll go away after you fix the initial cause by doing the update. Hope this gets it working smoothly for you, Brad