On Fri, Oct 24, 2014 at 10:18 AM, Lukasse, Pieter <pieter.luka...@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 > > > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
