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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 DEBUG 2011-07-26 17:01:04,762 job 4915 ended
I tried changing permission in __init__.py as mentioned in
I saw Erick has the same problem, and looks like he got a fix as mentioned
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