On Mon, Jan 25, 2016 at 3:33 PM, John Chilton <jmchil...@gmail.com> wrote:
> On Mon, Jan 25, 2016 at 3:26 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> 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)?
>
> 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.

Thanks John,

In that case is there a bug that external_chown_script.py gets
called unconditionally, when it should only happen for the drmaa
and pulsar runners?

Peter
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