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.gruening@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.gruening@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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