On 4 September 2015 at 21:00, Christian Brenninkmeijer < christian.brenninkmei...@manchester.ac.uk> wrote:
> I wrote the tool because when I ran planemo it found the tool_depencecy > file but then logged that it could not find the actual tools. > > So > 1. Did you install the dependecies into the galaxy you are using to run > planemo? > If not my tool will not work until you do. > > I didn't do this - how do I do this? Do I install the modules into the --tool_dependency_dir ? > 2. When you run the test does the log show it looked for but could not > find python_nltk_tools? > If not then the error is outside of the scope of the tool. > > Yes, it said: galaxy.tools.deps DEBUG 2015-09-04 20:55:32,054 Building dependency shell command for dependency 'python_nltk_tools' galaxy.tools.deps.resolvers.unlinked_tool_shed_packages DEBUG 2015-09-04 20:55:32,054 Unable to find dependency,'python_nltk_tools' '1.0' 'package' galaxy.tools.deps WARNING 2015-09-04 20:55:32,054 Failed to resolve dependency on 'python_nltk_tools', ignoring Thanks, Steve > Christian > ------------------------------ > *From:* Steve Cassidy [steve.cass...@mq.edu.au] > *Sent:* Friday, September 04, 2015 11:41 AM > *To:* Christian Brenninkmeijer > *Cc:* galaxy-dev@lists.galaxyproject.org > *Subject:* Re: [galaxy-dev] planemo and tool dependencies > > Thanks Christian, > I'm not sure I understand how to make use of this. My tool dependency > is described in an XML file which is in the same source directory as the > tool xml and python files. The tool xml file contains: > > <requirement type="package" > version="1.0">python_nltk_tools</requirement> > > and the tool_dependencies.xml file contains the definition: > > <tool_dependency> > <package name="python_nltk_tools" version="1.0"> > ... > > how do I tell planemo to tell galaxy that it should refer to this tool > dependency file to resolve the requirement? At the moment it's loading all > of the tools but doesn't seem to be concerned that the requirement isn't > met. > > Thanks for your help. > > Steve > > > > On 3 September 2015 at 18:06, Christian Brenninkmeijer < > christian.brenninkmei...@manchester.ac.uk> wrote: > >> Hi, >> >> I wrote an extension that will help planemo pull in tool dependencies. >> >> See >> https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py >> >> It is for when the dependency was installed into galaxy but where planemo >> is not using the database to find that tool. >> >> It works my helping planemo guess where the tool dependency may be. >> >> Hope that helps. >> Christian >> University of Manchester >> ------------------------------ >> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on >> behalf of Steve Cassidy [steve.cass...@mq.edu.au] >> *Sent:* Thursday, September 03, 2015 9:00 AM >> *To:* galaxy-dev@lists.galaxyproject.org >> *Subject:* [galaxy-dev] planemo and tool dependencies >> >> Hi all, >> I'm trying to test some tools under planemo and can't find out how to >> have it install tool dependencies while setting up the environment. >> >> The dependency is on a particular python module and we have a >> tool_dependencies.xml file to describe it. I can't see a way to tell >> planemo serve etc to refer to that file to get the dependencies. >> >> Any help appreciated. >> >> Steve >> >> -- >> Department of Computing, Macquarie University >> http://web.science.mq.edu.au/~cassidy/ >> > > > > -- > Department of Computing, Macquarie University > http://web.science.mq.edu.au/~cassidy/ > -- Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy/
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