Ann Black wrote:
> Thanks Nate! I did not know about sge_request - and that helps.  I played 
> around with using -V and -v in sge_request some and it works similar to 
> specifying -V (or -v) in my universe_wsgi.ini file.  I am new to galaxy and I 
> am working on getting it instantiated locally.  Is there an advantage to 
> setting my native DRMAA options in my galaxy user's  local .sge_request file 
> vs. directly in the universe_wsgi.ini configuration file?  Would an advantage 
> be that I can set more universal drmaa native options that I would like to 
> common for all tools there (sge_request for galaxy user) vs. duplicating the 
> in each per tool configurations in universe_wsgi file? 

Hi Ann,

It probably doesn't matter whether you use .sge_request or the runner
URL in the Galaxy config.  The difference may simply be that
.sge_request would be a little less messy.

--nate

> 
> Thanks again,
> 
> Ann
> 
> On Sep 12, 2011, at 12:50 PM, Nate Coraor wrote:
> 
> > Ann Black wrote:
> >> I figured out a solution.  The sun grid engine will strip back the env of 
> >> what gets passed along with the job submission.  I added a native drmaa 
> >> option, -V, which caused the env vars found on the shell that submits the 
> >> job to be passed along.  Therefore all the environment setup I did in my 
> >> galaxy user's .bash_profile and thus configured in my local shell running 
> >> galaxy now gets propagated with my job submissions.  This does not allow 
> >> changes to .bash_profile to be picked up dynamically, however, since the 
> >> .bash_profile is not sourced on each compute node.  IE changes made to the 
> >> galaxy user's env needs to be re-sourced in the shell that runs galaxy and 
> >> dispatches the jobs.
> >> 
> >> Thanks - hope this helps others,
> > 
> > Hi Ann,
> > 
> > For SGE, you can also use ~/.sge_request to set up the environment on
> > the execution host.
> > 
> > --nate
> > 
> >> 
> >> Ann
> >> 
> >> 
> >> On Sep 12, 2011, at 10:09 AM, Ann Black wrote:
> >> 
> >>> Hello everyone -
> >>> 
> >>> I am also running into this issue trying to get galaxy integrated with 
> >>> our sun grid engine.  My galaxy user's .bash_profile does not appear to 
> >>> get sourced when the jobs run. I augmented the sample sam_filter.py 
> >>> tutorial such that it output path and user info so I could see how the 
> >>> jobs were being run:
> >>> 
> >>> out = open( sys.argv[2], "w" )
> >>> out2 = open("/data/galaxy-dist/ann.out", "w")
> >>> out2.write(socket.gethostname())
> >>> out2.write("\n")
> >>> out2.write(os.environ['PATH'])
> >>> out2.write("\n")
> >>> drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
> >>> if drmaa is None:
> >>>  out2.write("None")
> >>> else:
> >>>  out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
> >>> out2.write("\n")
> >>> out2.write(str(os.geteuid()))
> >>> out2.write("\n")
> >>> out2.write(str(os.getegid()))
> >>> shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
> >>> 
> >>> the job is being dispatched as my galaxy user, however the my augments to 
> >>> PATH and additional env vars that I have exported in our galaxy user's 
> >>> .bash_profile are not present when the script runs (ie, .bash_profile is 
> >>> not sourced).  When I use qsub to manually run the galaxy script that 
> >>> gets generated under database/pbs, the output to ann.out reflects my PATH 
> >>> and exported env vars.
> >>> 
> >>> Was there any other solution to this issue besides the drmaa.py script 
> >>> augment?
> >>> 
> >>> Thanks much for your help,
> >>> 
> >>> Ann
> >> 
> >> 
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