On Mar 19, 2012, at 9:34 AM, Peter Cock wrote:

On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:

With regard to tool validity, the definition of a valid
tool in the tool shed has always been restricted to the tool properly
loading in a Galaxy instance.  If a tool is not valid, it will not be
returned in a search and it cannot be automatically installed (unless it
belongs to a repository containing other valid tools).  I'll consider ways
to list invalid tools contained in repositories in the tool shed, but the
preference is for tool developers to share only valid tools

I see - I hope you can make some improvements for browsing the tool
shed for this kind of situation.

Invalid tools are now displayed in the "Preview tools and inspect metadata by tool version" section - here is the list for the hmmer repository.

Preview tools and inspect metadata by tool version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Compress profile db1.0.0none
Invalid tools - click the tool config file name to see why the tool is invalid

If you click on the invalid tool, the error message is displayed - if the tool can be displayed it is...

This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error.

hmmer (version 1.0.0)
This can greatly reduce the output volume
The default is 0.01, meaning that on average, about 1 false positive would be expected in every 100 searches with different query subsequences.

Note. Hidden Markov Model (HMM) searches take a substantial amount of time. For large input datasets it is advisable to allow overnight processing.

What it does

hmmscan is used to search sequences against collections of profiles. For each sequence in seqfile, use that query sequence to search the target database of profiles in hmmdb, and output ranked lists of the profiles with the most significant matches to the sequence.

hmmsearch is used to search one or more profiles against a sequence database. For each profile in "hmmfile", use that query profile to search the target database of profiles in "seqdb", and output ranked lists of the sequences with the most significant matches to the profile.

If using a user-supplied profile database, it needs to be pressed using hmmpress before it can be searched with hmmscan.


Sean Eddy, Howard Hughes Medical Institute and Dept. of Genetics, Washington University School of Medicine