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.

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.

<<attachment: golharam.vcf>>

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