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/
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