Deploying galaxy instances using docker

Question: Deploying galaxy instances using docker

2.8 years ago by

tra • 50

United States of America

tra • 50 wrote:

This is a request for comments on a galaxy deployment strategy.

I am going to deploy a galaxy server for a whole department. Different groups have different requirements. Chief among them, I might want to maintain datasets on disk volumes that belong to different groups.

I was actually thinking in deploying a galaxy instance per research group. I know that this might sound vaguely crazy, but with docker it is actually quite lightweight in terms of admin. There would be a Dockerfille per group, tailored for each use case.

Does this sound that crazy as a general strategy?

Thanks for any comments

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modified 2.8 years ago by Bjoern Gruening ♦ 5.1k • written 2.8 years ago by tra • 50

2.8 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

I think this depends heavily on the amount of groups you need to support and the way you imagine to maintain your Galaxy server.

We are supporting approximately 30 groups as of today with ~300 researchers and for us it is easier to maintain one instance for all. Also because we try to run Galaxy in reproducible mode, this means we keep old versions of tools, data, workflows and so on ... If you want to run Galaxy in "run-and-kill" mode, Docker is a very good solution even for a large user-base.

Don't know if you know this project, but here you have a Galaxy Docker container with all what you need.

https://github.com/bgruening/docker-galaxy-stable

This one is used by many working groups in reproducible-mode, but they maintain them by there own, more or less for one group or as dedicated webserver (NAR-webserver issue) to suite one task. I also know one project that is offering a handful of Galaxy flavours in a web-browser. You can pick for example an RNA-seq flavour and gets redircted to your personal Galaxy instance. Use it once and kill it afterwards. This is nice for the 'move tools to your data' idea.

Here is a (incomplete) list of already existing Galaxy flavours:

https://github.com/bgruening/docker-galaxy-stable/tree/16.01#list-of-galaxy-flavours

and here is our first attempt to click together your own flavour without knowledge of Dockerfile:

http://galaxyflavorsgenerators.github.io/galaxyFlavorGenerator/

Hope this helps,

Bjoern

ADD COMMENT • link written 2.8 years ago by Bjoern Gruening ♦ 5.1k

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