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
> >~/.bash_profile
> 
> 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.

> 

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