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, "w" )
out2 = open("/data/galaxy-dist/ann.out", "w")
drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
if drmaa is None:
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,
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