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 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 
If not then the error is outside of the scope of the tool.

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" 

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 met.

Thanks for your help.


On 3 September 2015 at 18:06, Christian Brenninkmeijer 

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 
 on behalf of Steve Cassidy 
Sent: Thursday, September 03, 2015 9:00 AM
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
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