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
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