Hi Tiago, Am 03.08.2015 um 15:44 schrieb Tiago Rodrigues Antao: > 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.
!!! I know of a computer centers that are developing an interface where the user can choose a Docker container, based on their needs. So this is definitely possible > 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). I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :) > If there is any opinion on this approach, it would be appreciated. I don't think on container that fits all is good for usability, let's create small special ones. > I am actually thinking in developing a very small GUI to configure the > Dockerfile (say with users and cluster configuration) before build/run. Uh nice! Martin Page and Jeroen Galle are currently working on a Galaxy flavour generator: http://wookoouk.github.io/galaxyFlavorGenerator/ Maybe we could exchange ideas here? Thanks for you mail, Bjoern > 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 >>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" in your >>>>> mail client. To manage your subscriptions to this and other >>>>> Galaxy lists, please use the interface at: >>>>> https://lists.galaxyproject.org/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
