Maybe too obvious but something we have encountered before with other scripts.

Check that galaxy can find the requirements to run your script. Shell settings like PATH.

What we do when starting galaxy is to source the /etc/profile

Since galaxy is not using the ENV of for instance bash.

Hope this helps.

Alex

Van: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] Namens Makis Ladoukakis
Verzonden: dinsdag 12 februari 2013 11:54
Aan: galaxy-user@lists.bx.psu.edu
Onderwerp: [galaxy-user] Rscript not found when running shell script in Galaxy

Dear users,

Has anyone encountered this problem before? I wrote a shell script which among other things calls some R scripts like this..

Rscript rscript_to_use.R

When I run it via terminal it's fine plus I have verified Rscript works. But when I upload my tool to Galaxy and try to run it I get the following error:

/path/to/script/shell_script.sh: line 26: Rscript: command not found


Can anyone help?

Thank you in advance,
Makis Ladoukakis