Those changes to permission in __init__.py  are only necessary of running the 
job as the actual logged in user and not as the galaxy user. There are 
additional changes that are needed to get actual user name integration to work 
with SGE.

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of ambarish biswas
Sent: Monday, July 25, 2011 11:12 PM
To: galaxy-dev@lists.bx.psu.edu"
Subject: [galaxy-dev] galaxy sge Job output not returned from cluster

Hi All,
          I'm getting this error "Job output not returned from cluster"


galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state 
change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state 
change: job is running
139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST 
/galaxy/root/history_item_updates HTTP/1.1" 200 - 
"http://bioanalysis.otago.ac.nz/galaxy/history"; "Mozilla/5.0 (X11; U; Linux 
x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205 
Safari/534.16"
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state 
change: job finished, but failed
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not returned 
from cluster
galaxy.jobs<http://galaxy.jobs> DEBUG 2011-07-26 17:01:04,762 job 4915 ended


I tried changing permission in __init__.py as mentioned in
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html

but no luck.


I saw Erick has the same problem, and looks like he got a fix as mentioned
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html

but no detail of what should be done.

Thanks in advance.



With Regards,
----------------
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866

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