On Tue, Jun 7, 2011 at 9:24 AM, Mariette <jmari...@toulouse.inra.fr> wrote:
>
> Thanks for the answer,
>
> so I tryed to write a wrapper, but the main script is not recognize.
> When I'm calling my wrapper in the xml file, I don't have to specify
> the full path but then from my wrapper if I want to call my main script
> I can't if this one is not on the PATH ? the wrapper current directory
> is the job_working_directory, there is anyway to access my main script
> just like it's done for the wrapper ?

Generally put the wrapper script next to your tool XML file, and don't
prefix it with any path in the <command> tag in the XML, e.g.

/opt/galaxy/tools/mariette/my_tool.xml
/opt/galaxy/tools/mariette/my_tool.sh

(or my_tool.py or my_tool.pl etc depending on what language you used)

Your wrapper script then has to call the real executable, and the
normal way to do this on Unix is to have it on the PATH. You could
also hard code an absolute path.

Peter
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