Hi Greg,

   Thanks for the feedback. I cannot seem to find information for
hmmdb.loc.  When I look in the associated xml file it looks like it could
be removed completely (does one need a precompiled HMM Database? I do not
remember using anything like this when I run hmmer on the commandline).  I
have less experience with changing wrappers, etc. Have you tried just
commenting this part out?  And do I need to start the instance over to test
it?

Thanks in advance!
- Karen

    <conditional name="hmmdb">
        <param name="select" type="select" label="HMM Db">
          <option value="db" selected="True">Precompiled HMM
Database</option>
          <option value="user">HMM Database in your History</option>
        </param>
        <when value="db">
            <param name="file" type="select" label="Precompiled HMM
database">
                <options from_file="hmmdb.loc">
                    <column name="name" index="1"/>
                    <column name="value" index="2"/>
                </options>
            </param>
        </when>
        <when value="user">
            <param name="file" type="data" format="hmmer" label="HMM
database" />
        </when>
    </conditional>


On Sun, Dec 1, 2013 at 5:32 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> 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*<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&id=e7e502574a48abf0&async=false&show_item_checkboxes=false&f-free-text-search=hmmer&page=1>
> NameDescriptionVersion
> hmmpress<http://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e7e502574a48abf0&render_repository_actions_for=tool_shed&tool_config=database%2Fcommunity_files%2F000%2Frepo_148%2Fhmmpress.xml&changeset_revision=c0fb858f44a2>
> Compress profile db1.0.0
>
> Invalid tools* - click the tool config file name to see why the tool is
> invalid*<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&operation=view_or_manage_repository&id=e7e502574a48abf0&async=false&show_item_checkboxes=false&f-free-text-search=hmmer&page=1>
> hmmer.xml<http://toolshed.g2.bx.psu.edu/repository/load_invalid_tool?repository_id=e7e502574a48abf0&render_repository_actions_for=tool_shed&tool_config=hmmer.xml&changeset_revision=c0fb858f44a2>
>
>
> 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
> ___________________________________________________________
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>
>


-- 
Karen H. Miga, PhD

Postdoctoral Scholar
University of California, Santa Cruz
(831)459-5232
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