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
>>>> 
>>> 
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