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. > > begin:vcard > fn:Ryan Golhar, Ph.D. > n:Golhar;Ryan > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > email;internet:golha...@umdnj.edu > title:NGS Bioinformatics Specialist > tel;work:(732) 235-6613 > tel;fax:(732) 235-6267 > tel;cell:(732) 236-1176 > x-mozilla-html:FALSE > url:http://www.cinj.org > version:2.1 > end:vcard > > _______________________________________________ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/