Re: [galaxy-dev] Dependencies not working on toolshed?

24 Oct 2014

      Hi Bjoern, John,

thanks, this worked! 

So: I have to add a repository dependency to my tool_dependencies.xml file and NOT to my repository_dependencies.xml....I must say it is somewhat confusing. Somehow I had this idea that tool_dependencies.xml was for external tools.... But I'm happy it finally works!

Thanks again,

Pieter.

-----Original Message-----
From: Björn Grüning [mailto:bjoern.gruening@gmail.com] 
Sent: vrijdag 24 oktober 2014 16:23
To: Lukasse, Pieter; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Dependencies not working on toolshed?

Pieter,

please try to add your dependencies to a tool_dependencies.xml file not the repository_dependencies.xml file.

repository_dependencies.xml is for datatypes and for workflow dependencies, such things that need to be there, but that are not referenced from the tool.

Hope this helps,
Bjoern

Am 24.10.2014 um 16:18 schrieb Lukasse, Pieter:
...
Hi ,
I am trying to get a dependency to work in practice (when running a tool after the installation). But I keep getting the following message when running the tool:
[sshexec] galaxy.tools.deps DEBUG 2014-10-24 16:04:15,514 Building dependency shell command for dependency 'R_bioc_metams'
  [sshexec] galaxy.tools.deps WARNING 2014-10-24 16:04:15,514 Failed 
to resolve dependency on 'R_bioc_metams', ignoring
This is the tool requirements section:
<requirements>
              <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
       </requirements>
This is the repository_dependencies.xml :
<repositories description="Required metaMS dependencies.">
  <repository toolshed="http://testtoolshed.g2.bx.psu.edu"
  name="prims_metabolomics_dependencies" owner="pieterlukasse" 
changeset_revision="71356c62e5cd" /> </repositories>
This is the package name of the package that is being referred:
<tool_dependency>
 <package name="R_bioc_metams" version="3.1.1">
      <install version="1.0">
          <actions_group>
....
I can't find the problem. Any ideas? I have updated to the latest Galaxy version (today) and removed both items (with option to remove files) and installed them again. Am I facing a bug here?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International Department of 
Bioinformatics (Bioscience) Wageningen Campus, Building 107, 
Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl<http://www.pri.wur.nl/>
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