You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid:
Contents of this repository
If you click on the invalid tool in the tool shed, you'll see the reason that it is invalid:
hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error.
You should also see an exception thrown in your paster when you start your Galaxy instance telling you why the tool is not being loaded into Galaxy.
It look like this repository is missing a file named hmmdb.loc.sample that should provide sample entries for the Galaxy data tables that this tool must use. I'm not sure of the layout of this table for this particular tool, but if you discover what it should be, you can manually add them into a file named hmmdb.loc in the ~/tool-data directory in your Galaxy environment.
Greg Von Kuster
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