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/463852762a6eeadcf177312330ad1cd01053263d


> 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
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