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, Carlos ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
