On Tuesday, March 6, 2012, Edward Kirton <eskirton@lbl.gov> wrote:
> i gave it a bad name previously and peter didn't find it in a
> search at first, but i couldn't change the name, so i created
> a new repository.  i put a note in the old repo (hmmscan),
> referring to the new repo (hmmer).  that may suffice. however
> you folks how you want to handle it is fine.

Surely once the description was updated a search on hmmer
would find the old repository? Well anyway, now there are
two there should be a way to hide or deprecate one.

On a related note, I have a couple of old tools in the ToolShed
which I have just labeled as deprecated in the description
(and if memory serves, marked as hidden in the XML, so
existing workflows and history's can still run the tool, but
no new usage should be possible).