----- Original Message -----
> From: "John Chilton" <jmchil...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: galaxy-dev@lists.galaxyproject.org
> Sent: Monday, November 24, 2014 9:30:50 AM
> Subject: Re: [galaxy-dev] more control over the "docker" command
> 
> On Mon, Nov 24, 2014 at 10:54 AM, Dan Tenenbaum
> <dtene...@fredhutch.org> wrote:
> > 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?
> 
> 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 -
> https://bitbucket.org/galaxy/galaxy-central/commits/ebceda0721f3f3215447c19f94525f06f164afd1.
> 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.

Thanks very much for the quick turnaround!

I think it will work out. I am not an expert in job_conf.xml. My main concern 
is being able to pass extra arguments to some docker-enabled tools but not to 
others, is that possible?


> 
> >
> > 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
> destination parameter:
> 
>   <param id="docker_sudo">false</param>
> 
> 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.

Great, thanks. Actually, as was pointed out here (and as I realize now), 
adding the galaxy user to the docker group is not necessarily safer
(though it superficially looks like it because the word 'sudo' disappears).
So I think perhaps docker_sudo should remain true by default.

> 
> At any rate - keep us informed about how things are going - I would

I will let you know how it goes.

> love to hear about what you are attempting to do with the linked
> persistent docker container :).

Briefly, our tool is an R script that loads several R packages and then 
performs a calculation based on user input.
The problem is that it can take several minutes just to load the packages 
required to perform the calculation, 
but the calculation itself only takes a couple of seconds. Fast performance is 
important to us, so we set up
an instance of R that already has the packages loaded and we "serve" it using 
the Rserve package. So now the galaxy tool just has to send an expression to 
Rserve which can evaluate it quickly and reduce the tool running time from 
minutes to seconds. We are already using this setup in a non-docker context and 
your change now (I hope) enables us to do this with Docker.

Dan


> 
> -John
> 
> >
> > Thanks,
> > Dan
> >
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