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_python_2_7_10 >> 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.schae...@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.schae...@phe.gov.uk >>> http://www.gov.uk/phe >>> Protecting and improving the nation’s health >>> >>> ************************************************************************** >>> The information contained in the EMail and any attachments is confidential >>> and intended solely and for the attention and use of the named >>> addressee(s). 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