On Feb 18, 2011, at 2:12 PM, 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 use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE? > > 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. > <golharam.vcf><ATT00001..txt> -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/