IRIDA web installation to use Docker

[tom114]

We've had some complaints about the moderate difficulty of setting up the IRIDA web application, and some hassle during the update procedures. Some of this could possibly be simplified by building the IRIDA web front into a Docker container that we can manage and update on DockerHub instead. To be worthwhile the docker installation would have to have the following features:

• Easier initial setup than what we have now. This should be pretty straightforward as the Tomcat install can be a bit foreign to some admins.
• Ability to use external database + directories. We would still want to allow admins to link IRIDA to an external database server and mount a directory outside of the container for storage of sequence files.
• 1 click upgrade. Well maybe not exactly 1 click, but it should mean simply shutting down the docker container, re-pulling the latest image, and restarting. This leads to...
• Automated backups. The new package should be able to automatically back-up the database, config files, and maybe .war files. This should be both on upgrade and maybe on a scheduled basis.

Imported from GitLab issue #502. Originally posted on 2017/07/10 03:59PM

[dfornika]

I've created this docker-compose setup that runs IRIDA, MariaDB & Galaxy in three containers and hooks them up together.

https://github.com/dfornika/irida-docker

It could use a bit more work to make it as configurable as you've described above, but it might be a good starting point if you don't have something put together already?

[tom114]

Hey @dfornika , thanks for showing this off! I haven't had a chance to try it yet but it looks like a good start. The description I had above of using Docker for the full install of IRIDA was probably a bit of a dream. I know we've got some other things in the works for deployment automation so it might be a bit of a stretch to go that far. At the very least what I think this could be good for though is for a replacement/addition/build tool for the "try out IRIDA" VM we've been using for the last number of years. The VM is starting to get pretty unwieldy, and using something like Docker might ease things a bit. I'm going to try to get a look at this more in the next couple days.

[apetkau]

That's awesome. Thanks so much @dfornika :smile:. I haven't had a chance to try this out yet either. It's really cool you spent some time trying to get this working.

[kbessonov1984]

@tom114 @apetkau Hello all, I've developed even simpler solution that can run fully functional IRIDA 19.09 and Galaxy 19.05 with minimal configuration using a single docker image. In this image all official workflows are being tested, debugged and are fully functional. This image could be used to quickly deploy IRIDA in other labs as a demo or functional instance or to start working on developing new IRIDA pipelines as one can quickly check logs from Galaxy and IRIDA, etc. Please take a look at https://hub.docker.com/r/kbessonov/irida-dev-server. Hopefully it will save time for others.

[thanhleviet]

Hi @kbessonov1984 , the password for IRIDA docker is not working [https://hub.docker.com/r/kbessonov/irida-dev-server] . Could you take a look? Thanks

[kbessonov1984]

Try the following login for the local IRIDA instance: user name admin and password Password1!. In the password, the letter P is capital and a is a letter (not symbol @). I've tried to login and it for version tags 19.05.1 and latest. Let me know if it works

[thanhleviet]

Thanks @kbessonov1984 , it works.

[apetkau]

There exists some additional work with IRIDA and Docker at https://github.com/COMBAT-TB/irida-galaxy-deploy (thanks @pvanheus and @zipho and others).

[apetkau]

Also https://github.com/brinkmanlab/irida-container (thanks @innovate-invent)