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 ___________________________________________________________ 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/
