On 4 September 2015 at 21:00, Christian Brenninkmeijer <
> 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.
> 1. Did you install the dependecies into the galaxy you are using to run
> 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
> 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
> *From:* Steve Cassidy [steve.cass...@mq.edu.au]
> *Sent:* Friday, September 04, 2015 11:41 AM
> *To:* Christian Brenninkmeijer
> *Cc:* firstname.lastname@example.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"
> and the tool_dependencies.xml file contains the definition:
> <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
> Thanks for your help.
> On 3 September 2015 at 18:06, Christian Brenninkmeijer <
> christian.brenninkmei...@manchester.ac.uk> wrote:
>> I wrote an extension that will help planemo pull in tool dependencies.
>> 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.
>> 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:* email@example.com
>> *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.
>> Department of Computing, Macquarie University
> Department of Computing, Macquarie University
Department of Computing, Macquarie University
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