On Mon, Jan 25, 2016 at 4:44 PM, John Chilton <jmchilton@gmail.com> wrote:
I think the problem is more that it is configured globally and not per-destination. The real user stuff should all be per-destination and not globally configured - since it should be possible to have like a dedicated cluster for Galaxy jobs that just run jobs normally and a general purpose cluster that submits jobs as the real user for accounting purposes.
Excellent point.
I have created a WIP pull request to move the configuration of these options in that direction:
https://github.com/galaxyproject/galaxy/pull/1573
I haven't tested any of the changes in the PR yet - I just wanted to open something to ensure I'd come back and finish things this cycle.
It is something that I have wanted to do for a while now - see https://trello.com/c/6w8bples. In general there are a bunch of Galaxy options for jobs that can only be configured in galaxy.ini but that you may wish to have different values for depending on the job destination.
That makes a lot of sense :)
You are going to want a smaller hack that can be backported just to run the local job runner when that option is configured huh?
-John
i.e. Only attempt to call external_chown_script.py for the drmaa and pulsar runners? The full fix looks more involved and likely to take a while to gestate. If you think it sensible to get a quick hack into the main development branch now (and the next stable release), that would be handy. Has anyone else hit this problem, and how did you solve it? We're considering trying an alternative of using SGE with a separate queue consisting of just the Galaxy server, as a substitute for the local worker - but we won't have a chance to try that till next week. Peter