On Mon, Jan 25, 2016 at 3:26 PM, Peter Cock email@example.com wrote:
On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock firstname.lastname@example.org wrote:
We're currently looking at changing our Galaxy setup to link user accounts with Linux user accounts for better cluster integration (running jobs as the actual user on SGE). As part of this, we've tried setting up a fresh installation on a new VM which has thrown up some issues.
We eventually got Galaxy to talk to SGE and submit jobs successfully as the individual user's Linux account, with external_chown_script.py being called to handle ownership of the files.
However, we would like to have some jobs (like the upload tool) configured to run on the Galaxy server itself - and the easiest way to do that is via the local job runner.
We tried both the "upload1" and "Convert characters1" tools. These jobs would start and seem to run, but then fail with a file permission error (I don't have a stack trace to hand). From watching the Galaxy terminal output from run.sh we could see external_chown_script.py being called.
As a test, when we disabled the external_chown_script setting in config/galaxy.ini then the local jobs would work.
When using the local job runner, does Galaxy run the child process as the Galaxy user (my guess - no chown needed), or as the job owner's Linux account (calling chown would be needed)?
Yes, only the drmaa and pulsar runners really support running jobs as a different user. The local job runner pretty explicitly will only ever run as the Galaxy user.
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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