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,


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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