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
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
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
participants (3)
-
Bossers, Alex -
Carlos Borroto -
Makis Ladoukakis