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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