On Fri, Oct 24, 2014 at 10:18 AM, Lukasse, Pieter pieter.lukasse@wur.nl wrote:

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>

In my limited understanding repository_dependencies.xml is for stuff like datatypes where the dependencies are implicit, but for something like this you need to put a tool_dependencies.xml file in the repository not a repository_dependencies.xml.

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

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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.nlhttp://www.pri.wur.nl/

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On Fri, Oct 24, 2014 at 10:17 PM, Lukasse, Pieter pieter.lukasse@wur.nl wrote:

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.

You are not alone - I have regularly messed this up, but at least once you know of this pitfall it will be easier to spot the problem in future. It is one of the first things I check if I have a dependency problem shown up via the ToolShed tests.

Regards,

Peter