Hi,

I am also thinking in doing something similar.

My idea would be to deploy a galaxy docker on demand per project. The
docker would have a galaxy installation that would be configured to
join a cluster. Most of the computation would actually occur on the
cluster.

Each project would thus have its isolated galaxy with separate users. I
am extending your docker file with all the tools from the toolshed (I
know, it will become a large one-size-fits-all installation).

If there is any opinion on this approach, it would be appreciated.

I am actually thinking in developing a very small GUI to configure the
Dockerfile (say with users and cluster configuration) before build/run.

Tiago


On Sun, 02 Aug 2015 10:23:20 +0200
Björn Grüning <bjoern.gruen...@gmail.com> wrote:

> Hi,
> 
> I will think about this, but this comes with the price of doing much
> of the internal stuff during startup, which also have it's downsides.
> 
> Can you tell me what your admin wants to do, maybe we find a solution
> without changing the build-time variables?
> For example we can talk to schedulers without changing UID/GID ...
> 
> Thanks for using Galaxy!
> Bjoern
> 
> Am 02.08.2015 um 05:19 schrieb Oksana:
> > Hi Bjorn,
> > 
> > Our team is trying to streamline our Galaxy development process, by
> > using your docker container for development, test and production
> > environments. To do that, our sys admin needs to be able to change a
> > few of Galaxy build time variables, like the ones that I've
> > mentioned and probably more, since our production is running on a
> > cluster and its setup will be quite different from the local dev.
> > We wouldn't want to modify the docker image from environment to
> > environment, so a config file, which would allow to set those build
> > variables before a container is built, would be really useful. Are
> > you planning to extend your development to accommodate this need in
> > the near future? Or if there is already a way to do this that I
> > don't see, please let me know.
> > 
> > Cheers, Oksana
> > 
> > 
> > 
> >> On Aug 1, 2015, at 1:10 PM, Björn Grüning
> >> <bjoern.gruen...@gmail.com> wrote:
> >> 
> >> Hi Oksana,
> >> 
> >> both variables are used during container build to create users and
> >> home directories. This does not happen during container startup.
> >> They are buildtime variables.
> >> 
> >> All Galaxy ENV vars are runtime variables and do have an impact
> >> during startup.
> >> 
> >> Can you tell us more about what you want to do? Thanks, Bjoern
> >> 
> >>> Hi,
> >>> 
> >>> My question is to the docker-galaxy-stable community. I would
> >>> like to use or extend this image with some Galaxy settings
> >>> externalized. For instance, I would like to define my own
> >>> GALAXY_UID and GALAXY_HOME environment variables. I have tried
> >>> the -e setting when I build and run the container, but that
> >>> doesn't work:
> >>> 
> >>>> docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e
> >>> "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test 
> >>> bgruening/galaxy-stable ...
> >>>> docker exec -ti  galaxy-env-test bash # getent passwd galaxy
> >>> galaxy:x:1450:1450:Galaxy user:/home/galaxy:
> >>> 
> >>> As you can see from above, GALAXY_UID is 1450, as hardcoded in
> >>> the Dockerfile, and not 1777, as I've specified. Same goes for
> >>> the home directory.
> >>> 
> >>> Is there any other way that I can set those variables? If not,
> >>> what would be the best way to proceed, since, ideally, I would
> >>> like to extend the galaxy-stable Docker image, and not change the
> >>> existing one. Currently, I don't see any other way but to fork 
> >>> https://github.com/bgruening/docker-galaxy-stable and change the
> >>> Dockerfile to externalize those (and other) variables. I hope I
> >>> can get better suggestions than this.
> >>> 
> >>> Cheers, Oksana
> >>> 
> >>> 
> >>> 
> >>> ___________________________________________________________ 
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