On Wed, Apr 15, 2015 at 2:34 PM, Björn Grüning <bjoern.gruening(a)gmail.com>
Am 07.04.2015 um 21:46 schrieb Michael Crusoe:
> On Wednesday, March 25, 2015, Björn Grüning <bjoern.gruening(a)gmail.com>
>> Hi all!
>> We are proud to present you the next release of Galaxy Docker.
>> A few highlights:
>> * based on Galaxy 15.03, with all it's new awesome features
>> * Docker image is now based on Ubuntu 14.04
>> * move all required Galaxy dependencies to toolshed/requirements
> * use Ansible roles to build large parts of the image
> Super cool. How many dependencies are you having to install from source
> instead of from Debian packages (either official or 3rd party)?
A few python packages from pypi, npm and a self-build nginx to get some
extensions in that are currently not available in the official build.
Neat. From personal experience I can tell you that packaging PyPI hosted
Python code is pretty straightforward. And
looks decent on that front.
> I think Docker has a lot of usefulness for complicated setups; for
> packaging I think making proper Debian packages benefits the entire
> bioinformatics community more. Bonus: you get a collaborative team (like
> the Debian Med group) to share the burden.
Sure, if you have any ideas what we can package? I don't think we have
much packages that are not from Debian :)
The above mentioned python packages, npm packages, and that nginx for
> I don't know what people's interest is in packaging tools and other
> dependencies for Debian but I'd be happy to talk about it informally;
> a formal talk; present a poster; and/or host a BoF on the topic at the
> Galaxy Community Conference in July.
I think that in general the entire problem of deployment is very
interesting for the Galaxy community and we have a lot of ideas how to
make it better in/with Galaxy. Not sure about Debians role here, as we
are aiming for a reproducible installation of tools over time.
package name + version + hash + http://snapshot.debian.org/
(as needed) =
Also: see https://wiki.debian.org/ReproducibleBuilds
I will organise a BoF at BOSC to talk in a more general way about
deployment w/wo docker, packages, bioboxes, brew, conda, easyinstall and
so on ... would be great if you can join!
Huzzah, I will be at BOSC & GCC both and will join in.
Thanks for caring!
Of course; cheers,
Michael R. Crusoe