Ryan Golhar wrote: > It turns out the user's environment is not set up for batch jobs, > only the system environment. I too added ". ~/.bashrc" to > lib/galaxy/jobs/runners/drmaa.py. > > I'm afraid this is a kludgy fix that will break if/when the drmaa.py > file gets updated. It'll work for now, but there has got to be a > better way.
I'll work on this and release a fix (or instructions for environment configuration) ASAP. > > > > On 2/18/11 1:30 PM, Zhibin Lu wrote: > >Hi, > > > >I had same problem since we do not install software in the system > >directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py > >manually. I do not know if anyone has better solution. > > > >Zhibin Lu > >Bioinformatics Support > > > >Ontario Institute for Cancer Research > >MaRS Centre, South Tower > >101 College Street, Suite 800 > >Toronto, Ontario, Canada M5G 0A3 > > > >www.oicr.on.ca > > > > > Date: Fri, 18 Feb 2011 13:17:26 -0500 > > > From: n...@bx.psu.edu > > > To: golha...@umdnj.edu > > > CC: galaxy-dev@lists.bx.psu.edu > > > Subject: Re: [galaxy-dev] cluster path question > > > > > > 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/ > > > > > > > >_______________________________________________ > >To manage your subscriptions to this and other Galaxy lists, please use the > >interface at: > > > > http://lists.bx.psu.edu/ > > -- > CONFIDENTIALITY NOTICE: This email communication may contain > private, confidential, or legally privileged information intended > for the sole use of the designated and/or duly authorized > recipient(s). If you are not the intended recipient or have received > this email in error, please notify the sender immediately by email > and permanently delete all copies of this email including all > attachments without reading them. If you are the intended recipient, > secure the contents in a manner that conforms to all applicable > state and/or federal requirements related to privacy and > confidentiality of such information. > 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/
