Thanks Martin and Bjoern for your advice.
Bjoern, does this modification to the galaxy.ini need to be made on all Galaxy instances that want to install and run this tool once its available in the shed? I assume it has nothing to do with the ability to publish it in the first place.
Thanks Ulf
On 01/12/15 16:41, Björn Grüning wrote:
Hi Ulf,
just adding to Martins great explanation that you should set
enable_beta_tool_command_isolation = True
in your galaxy.ini file if you are using a strict Python dependency with package_python_2_7_10.
Cheers, Bjoern
Am 01.12.2015 um 17:07 schrieb Martin Čech:
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)
The package is being developed here https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pyth... and is available at the MTS here https://toolshed.g2.bx.psu.edu/view/iuc/package_python_2_7_10/73631e818d3d
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.
On Tue, Dec 1, 2015 at 10:54 AM Ulf Schaefer Ulf.Schaefer@phe.gov.uk wrote:
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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