HI Brian, Thanks for sharing your code. We have just discussed your approach as one possibility of solving our problem, but delayed it as it involved too much hacking :). Now that you've done the hacking, we may revisit it. We were also discussing a possibility of creating access groups with Galaxy UID and cluster process ID to get around the permissions problem that Iyad has described. This would involve extra setup outside Galaxy container, but would possibly remove the need to change GID and UID. Will reply when we've solidified and tested our approach.
Bjorn, I would second Brian on being able to configure Galaxy for different environments. To us that was the primary reason of going the docker way. We have considered vagrant, since it seemed like a more mature and more flexible technology for running in production, but went with docker, because Galaxy community supports it. I would personally like to be able to change build-time variables at build, since it's more logical, requires less hacks and the build speed is not as important to me when building containers for different environments, since I'm not going to do that often. I.e.I would still have your lightweight way as a default, but allow to change it for those who need it. That said, I would welcome any standardized solution, be it run time or build time. Cheers, Oksana On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Brian, > > thanks for you mail! Very appreciated, please see my comments inline. > > >> We only have one cluster, so we will have both test and production > >> environments running on it. I understand that at a minimum we'd need > >> different Galaxy home dir and UID/GID. > > > > > > For our local deployment of Galaxy with Docker, which was inspired by a > > very early version of Björn's docker-galaxy-stable, we use an entrypoint > > script to remap the Galaxy user's UID and GID inside the container from > > environment variables GALAXY_UID and GALAXY_GID passed to `docker run`: > > Is this really needed. We could do this in the main image as well, but > currently I haven't seen a compelling usecase for this. The downside is > that we need to do a lot of `chown/chmod` magic during container startup. > But I'm totally willing to do so, if this is was the community is needed. > > Please also see this latest PR: > https://github.com/bgruening/docker-galaxy-stable/pull/71 > > > > https://github.com/fredhutchio/docker-galaxy/blob/aa07c5f684d55499a87e77c62aceda707b63077f/docker-entrypoint.sh#L30 > > > > Just below that, starting at line 42, is an admittedly hacky way of > > relocating the Galaxy directory hierarchy (exported data and/or code) > from > > its container default location /galaxy to another location specified by > the > > GALAXY_ROOT environment variable. It essentially turns the container into > > an installer when `--reroot` or `--upgrade` is passed to the entrypoint > > script. `--reroot` copies the container's entire /galaxy hierarchy to > > $GALAXY_ROOT for initializing an instance from the container. `--upgrade` > > copies just the container's Galaxy distribution in /galaxy/stable to > > $GALAXY_ROOT/stable (aka $GALAXY_HOME) for upgrading an existing instance > > from a more recent image. > > Interesting! > At least for easier upgrading we took a slightly different approach, > described here: > > https://github.com/bgruening/docker-galaxy-stable/tree/dev#upgrading-images > > Also we store nowadays many original config files in /etc/galaxy/ to > make the upgrading smoother. > I would be interested in your opinion and if these latest developments > would solve your use-cases. > > > It's definitely nice being able to configure things like this at runtime > > for e.g. differentiating between test and production! Would functionality > > like this be useful/welcome in docker-galaxy-stable? > > I'm all for it, if this is what is needed by the community. > I would just like to keep the initial startup magic by default as > minimal as possible. > > Thanks a lot for your comments, > Bjoern > > > > Cheers, > > > > Brian > > > -- :: Oksana Korol dataquarry.blogspot.ca
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