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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