Kyle, Brad, all,
Thanks for getting this conversation started, I am by no means a
Docker expert - but I have taken a shot at integrating it with Galaxy,
opened a pull request, and I am fairly excited about the result (by
all means though please tell me what I have done wrong and what needs
to be improved).
Like Kyle suggested it allows tools to annotated what image to use -
but Galaxy has all the inputs, outputs, and stuff annotated so I am
not sure an alternative command-line is needed. There is some
intelligence in there for determining what needs to be mounted
read-only and what needs to be mounted read-write - and that is all
extendable by the deployer - so library data and indices can be added
read-only say. If the Galaxy option outputs_to_working_directory is
enabled - the container should just need to write to the working
directory so that is reflected in the adaptive defaults as well.
Furthermore - if the LWR is being used even the inputs are staged (be
default anyway) so the container can be highly isolated - basically
just having read-only access to inputs and write access to its
This implementation disables the container's network access by default
- that coupled with the LWR isolation could potentially make tools
that take in arbitrary scripts more palatable. Lots of exciting
Looking forward to building some cool stuff with you guys at the hackathon!
On Tue, Jan 14, 2014 at 7:44 AM, Brad Chapman <chapmanb(a)50mail.com> wrote:
I'm also excited about Docker for easing installation issues and fully
capturing run environments. I haven't yet done anything specifically for
Galaxy tools but put together a functional docker installation of
bcbio-nextgen as a step towards integration:
The trickiest parts of integration are that you need to mount all
container-external data directories used, so need to identify inputs,
outputs and data files and map them over to mounts in the
There is some optimism about support for at least Mac for running
containers. There is a native Docker client, and work on supporting the
server side is on going according to the discussion:
There is also the approach using super minimal VMs that wrap
docker. This isn't easy to use yet but it looks like the proof of
concept is there:
It would be great to hear what other people end up doing with
Docker. Thanks for starting this discussion,
> I know a few people have talked about using docker to package and
> distribute Galaxy tools. The most recent version now runs on all major
> linux distributions, so it's a bit more inclusive now (but there probably
> won't ever be a windows or mac version). One strategy would be for tool
> configs to define an option Docker archive name and possibly an alternate
> command line to execute if the docker archive is being used.
> How far has that work gotten, and what are people thinking about it?
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