On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> 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.
> [snip]

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)?


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