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

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