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 <p.j.a.cock(a)googlemail.com>wrote:
On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga <khmiga(a)soe.ucsc.edu> 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
> Thanks in advance!
> - Karen
> <conditional name="hmmdb">
> <param name="select" type="select" label="HMM
> <option value="db" selected="True">Precompiled
> <option value="user">HMM Database in your
> <when value="db">
> <param name="file" type="select"
> <options from_file="hmmdb.loc">
> <column name="name" index="1"/>
> <column name="value" index="2"/>
> <when value="user">
> <param name="file" type="data"
> database" />
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.
Karen H. Miga, PhD
University of California, Santa Cruz