Thank you, Peter and Greg, for your feedback.

Unfortunately, I am still hitting a wall with the hmmer install - even
after creating a dummy hmmer.loc file and a hmmer.loc.sample file in my
tool-data dir.  All of my paths seem to be ok.  Has anyone gotten hmmer to
work on galaxy?  Do I need to restart my cloud instance? Should I get
instant feedback with the invalid hmmer.xml is valid, do I need to


On Mon, Dec 2, 2013 at 3:51 AM, Peter Cock <>wrote:

> On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga <> wrote:
>> 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>
> This lets the Galaxy HMMER wrapper either be used with system level
> HMM databases (listed in hmmer.loc, e.g. PFAM) or with the user's own
> HMM databases in their current history.
> [This is very similar to how the BLAST+ wrappers work.]
> If you don't have or need any standard HMM databases (e.g. PFAM)
> then an empty hmmer.loc file should work fine. Try that first.
> However, the tool author ought to provide an example named
> hmmer.loc.sample which explains how to set this up - it looks
> like two columns, description and filename.
> Peter

Karen H. Miga, PhD

Postdoctoral Scholar
University of California, Santa Cruz
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