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.
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.
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<mailto: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<mailto:galaxy-dev-boun...@lists.galaxyproject.org>]
on behalf of Steve Cassidy
[steve.cass...@mq.edu.au<mailto:steve.cass...@mq.edu.au>]
Sent: Thursday, September 03, 2015 9:00 AM
To:
galaxy-dev@lists.galaxyproject.org<mailto: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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