it is not so complicated :)
Try the following:
- define a ENV variable and export them in your tool_dependencies.xml
- import them as requirement in your my_tool.xml file
- use it with \$my_env_variable in your command tag.
A working example you can find here:
> 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
> 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
> Cell +27 72 073 6011
> Office +27 12 420 5802
> Fax +27 12 420 5800
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