On Mon, Nov 24, 2014 at 10:54 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> Thanks for supporting the running of docker containers in Galaxy.
> I have two requests for more control over the docker command that is run.
> According to https://github.com/apetkau/galaxy-hackathon-2014 , the docker
> command that is run when a docker-enabled tool is run might look something
> like this:
> command is: sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
> cts/galaxy-central:ro -v
> -v /home/aaron/Projects/galaxy-central/datab
> -v /home/aaron/Projects/galaxy-central/database/files:/home/aa
> ron/Projects/galaxy-central/database/files:rw -w
> --net none busybox:ubuntu-14.04
> return_code=$?; if [ -f
> rking_file ] ; then cp
> /home/aaron/Projects/galaxy-central/database/files/000/dataset_10.dat ; fi;
> sh -c "exit $return_code"
> I'd like to be able to specify extra flags to be included in the command. In
> my case I'd like to include "--link server:server" because I want to link
> this container with another container that contains a long-running server
> process (I can describe my use case in greater detail if desired).
> Can there be a way to do this in my tool wrapper?
I certainly don't mind adding more options - we've added a bunch as
different interesting things have been attempted (e.g. docker in
docker). I would like to keep the tool wrapper very general though and
expose these options in the job_conf.xml instead - since for the most
part they seem like they will be related to the tool's deployment and
not the abstract command being produced. I have added this
functionality with the following changeset -
Simply add <param id="docker_run_extra_arguments">--link
server:server</param> to your job destination. Let me know if this
doesn't work out.
> Secondly, rather than giving my galaxy user passwordless sudo, I'd like to
> add it to the docker group, then I can run docker commands without prepending
> sudo. This seems a lot safer. Could this be exposed, maybe by a sudo="false"
> attribute in the tool wrapper?
This is currently possible - in your job_conf.xml just add to the job
Checkout the admittedly huge file config/job_conf.xml.sample_advanced
for a full list of the supported options. The docker related options
are all near each other and apply to any built-in job runner.
I suspect tot running with sudo really should be the default and I am
growing frustrated it is not. I am unsure if I should "fix" it now and
break the couple sites doing Docker in Galaxy or just leave it and
have everyone who wants to turn sudo off disable it explicitly.
At any rate - keep us informed about how things are going - I would
love to hear about what you are attempting to do with the linked
persistent docker container :).
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