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 reinstall?
Karen On Mon, Dec 2, 2013 at 3:51 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > > > > On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga <khm...@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 >> 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 (831)459-5232
___________________________________________________________ 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/