Ryan Golhar wrote:
> >Ryan Golhar wrote:
> >>I'm setting up Galaxy to run on my cluster using drmaa. I can see
> >>jobs getting submitted to Torque however the jobs keep failing,
> >>because the tools are in the default system path.
> >>How do I tell galaxy to append a directory to the path used by jobs?
> >Hi Ryan,
> >Whatever user is running the jobs will need to modify the $PATH in its
> >shell startup files. If you're using bash, this would probably be
> It already is in .bashrc (which is called by .bash_profile) for the
> galaxy user. I can submit the script from the shell and it runs
> okay so something is up with either how the galaxy app is submitting
> the job or the environment being used by the galaxy job.
When you say submit via the shell, do you mean with qsub, or by logging
in to a node and running the wrapper script?
I haven't tested Torque with the drmaa runner so perhaps it's submitting
in a way which starts the shell in non-interactive, non-login mode. Let
me know if you can determine for certain that no shell startup files are
being read, and I'll try to replicate this in my environment.
> I'd like to modify the job script to print out some debugging
> information to determine what environment variables are set when the
> job gets executed. Actually, this would be a useful "tool" within
> Galaxy to test the cluster.
That's probably the simplest method, to just create a tool that outputs
(either to stdout or the output file) what you'd like to see.
> fn:Ryan Golhar, Ph.D.
> org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics
> adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA
> title:NGS Bioinformatics Specialist
> tel;work:(732) 235-6613
> tel;fax:(732) 235-6267
> tel;cell:(732) 236-1176
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