> We can hack the old wrapper back in, using a hard-coded path to the old 
> cuffdiff.

You could also use Managed Tool Dependencies for multiple versions of cuffdiff:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

> Shantanu suggests it might be a better world if we create a tool-shed 
> repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install 
> that.
> Would that be a better path, or just add confusion?

This is on the right path. The right thing to do is migrate the Cuff* tool 
wrappers out of the galaxy-central/dist repositories; this is a bit more effort 
than simply creating the tool-shed repository for the wrappers.

There are two reasons I haven't done this:

(a) time;
(b) because the tools—and consequently the wrappers—are still in active 
development, there needs to be a place for managing development of the 
wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the 
Galaxy team) haven't determined where these wrappers should live.

(a) is a much more significant barrier than (b), so if a pull request migrating 
Cuff* tools out of the distribution were made, I'm sure (b) could be worked out.

Best,
J.

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