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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/