On Tue, Feb 12, 2013 at 5:54 AM, Makis Ladoukakis makis4ever@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, Carlos