Hi Ulf,
you most probably want your tool to depend on package_python_2_7_10 from the iuc (it will ensure your tool has access to 2.7.10 no matter what python the Galaxy executing your tool is using)
You will need to add to your wrapper's xml something like:
<requirements>
<requirement type="package" version="2.7.10">python</requirement>
</requirements>
And you have to include tool_dependencies.xml file which will look something like:
<?xml version="1.0"?>
<tool_dependency>
<package name="python" version="2.7.10">
<repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
</package>
</tool_dependency>
Please let me know if you have more questions.
M.
Dear all
I have a Python script that I would like to publish to the tool shed. It
has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML).
It also needs a Python version 2.7<=X<3, which is not available per
default everywhere.
Firstly, how do I specify these dependencies in the tool <requirements> tag?
And secondly, once I have a correct set of tool definition files with
tests and test data, how do I best get it onto the tool shed?
I had a look through the wiki and the planemo documentation.
Unfortunately how to handle these dependencies did not become
immediately obvious (to me).
Thanks for any pointers and sorry if this has been answered some place I
did not look.
Cheers
Ulf
--
Ulf Schaefer, PhD
Bioinformatics Scientist
Bioinformatics Unit - Infectious Disease Informatics
National Infection Service
Public Health England
61 Colindale Ave, London NW9 5EQ
ulf.schaefer@phe.gov.uk
http://www.gov.uk/phe
Protecting and improving the nation’s health
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