Hello Karen, You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid:
Contents of this repository Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata Name Description Version hmmpress Compress profile db 1.0.0 Invalid tools - click the tool config file name to see why the tool is invalid hmmer.xml 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 On Dec 1, 2013, at 4:44 PM, Karen Miga <khm...@soe.ucsc.edu> wrote: > Hello, > > I would like to use hmmer on our cloudman instance. However, when I > install I am only finding a wrapper for hmmpress. There was some > conversation about this back in 2012 > (http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). > > > I installed the hmmer package 3.0 and 3.1 from the toolshed as well, > however, I am not seeing a wrapper for these tools - perhaps I am missing > something? > > Best wishes, > Karen > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
