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.
> 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
> Can you tell us more about what you want to do?
>> 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
>>> 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
>> 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.
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