Hi Jaenré, it is not so complicated :) Try the following: - define a ENV variable and export them in your tool_dependencies.xml file: <set_environment version="1.0"> <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - import them as requirement in your my_tool.xml file <requirement type="set_environment">SCRIPT_PATH</requirement> - use it with \$my_env_variable in your command tag. A working example you can find here: https://github.com/bgruening/galaxytools/tree/master/bismark_wrapper Cheers, Bjoern

Hi

We are in the process of creating a Galaxy Tool Shed repo and we need to know what the absolute path of the local installation of the repo is, inside a Python wrapper, since it's unique for every instance of Galaxy. We need this path in order to run an R script.

The only possible way we found on Google is by using the

galaxy.tool_shed.tool_dependencies.install_util.get_tool_shed_repository_install_dir(app, tool_shed_repository)

command, but as I understand it this command is only usable during the installation of a repository.

Is there any way to get the absolute path of the installation directory when a wrapper is executed?

Thanks in advance

-- Jeanré Smit

Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria 0002

Cell +27 72 073 6011 Office +27 12 420 5802 Fax +27 12 420 5800

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