On Tue, Feb 12, 2013 at 5:54 AM, Makis Ladoukakis
<makis4e...@hotmail.com> wrote:
> 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

Are you using a cluster to submit galaxy tasks? If so, you might want
to use '-V' in 'default_cluster_job_runner' ( I think this works for
SGE and Torque ) or  set 'environment_setup_file' and make sure $PATH
is correctly set by that method.

Also, in the future I would recommend sending these type of questions
about local or cloud Galaxy instances to galaxy-dev mailing list.

Hope it helps,
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