Hi,
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=$GALAXY_SLOTS" -v /home/aaron/Projects/galaxy-central:/home/aaron/Proje cts/galaxy-central:ro -v /home/aaron/Projects/galaxy-central/tools/docker:/home/aaron/Projects/galaxy-central/tools/docker:ro -v /home/aaron/Projects/galaxy-central/datab ase/job_working_directory/000/6:/home/aaron/Projects/galaxy-central/database/job_working_directory/000/6:rw -v /home/aaron/Projects/galaxy-central/database/files:/home/aa ron/Projects/galaxy-central/database/files:rw -w /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6 --net none busybox:ubuntu-14.04 /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/container.sh; return_code=$?; if [ -f /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/wo rking_file ] ; then cp /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/working_file /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?
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?
Thanks, Dan