Hi Pieter, think more about it from the actual name. tool_dependencies.xml for your tools (wrappers) and repository_dependencies.xml for your repository. Thinks that are only indirectly or not at all needed by your wrapper.
Glad it's now working for you! Bjoern Am 24.10.2014 um 23:17 schrieb Lukasse, Pieter: > 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.gruen...@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/> >> >> >> >> >> ___________________________________________________________ >> 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/
