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 <greg@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 <khmiga@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-hmme...).

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 ___________________________________________________________ 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/

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-- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232

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.cock@googlemail.com>wrote:

On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga <khmiga@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