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
command is: sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v
return_code=$?; 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?
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?
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