Consider Galaxy

[TuomasBorman]

Bioconductor aims to tighten links with Galaxy. Galaxy is a large ecosystem. If there is large movement towards Galaxy, we should also consider moving from CSC to Galaxy as it would perhaps serve more users and be more accessible.

E: Also good to keep an eye on this thing. We could consider also creating a RStudio there with all OMA packages and update the packages automatically if necessary (if that is possible to do). Currently, there are achieved workshops from past conferences.

[RiboRings]

Hi!

Thanks for the suggestion. That sounds like a good idea, as long as it doesn't require big changes in the current structure of the miaDash package.

Setting up the web app on CSC wasn't that easy and took me and @ake123 a few weeks to figure out completely (and still there are some things not working ideally). So it would be great to get help from someone already familiar with deploying shiny apps on Galaxy, otherwise testing it might take quite some time.

[ake123]

It seems a nice idea in the mean time we can start to figure out how to host it there. Is it free though?

[TuomasBorman]

Galaxy is free. There are currently some discussion in Zulip. Does this help: https://github.com/jaidevjoshi83/r2g2
We can also wait until someone else from Bioc has deployed their tools.

[RiboRings]

Thanks! I think that is to generate a (static) Galaxy tool from an R package. For example, it can be used to create a Galaxy tool for mia. However, miaDash and other shiny apps are dynamic so they can be reproduced with interactive Galaxy tools. This is a tutorial to create one, but in practice it might be cumbersome: https://training.galaxyproject.org/training-material/topics/dev/tutorials/interactive-tools/tutorial.html

[RiboRings]

Tagging @artur-sannikov as he might have insights and be interested in this.

[artur-sannikov]

We could consider also creating a RStudio there with all OMA packages and update the packages automatically if necessary (if that is possible to do).

It's already available with Docker images, but do you mean to create it on Galaxy?

[RiboRings]

Yes, at leat Galaxy interactive tools can be created from Docker containers. In practice, I see two possible uses of Galaxy:

1. Host miaDash as an interactive tool
2. Create non-interactive mia tool

Since we already have an app (miaDash), option 1 is probably more useful and option 2 is not really needed.

But we might move at least miaDash from CSC to Galaxy at some point.

[artur-sannikov]

I think this is what's need to be created: https://galaxyproject.org/toolshed/tool-features/

It is then possible to run Galaxy in Docker.

[RiboRings]

I realised that what we can get out of Galaxy and CSC isn't exactly the same.

On the one hand, CSC provides a publicly available instance of miaDash, which any user can access at any moment. On the other hand, Galaxy would provide an on-demand instance of miaDash, which is user-specific and not continuously deployed online.

It might still be useful to add miaDash to Galaxy as an interactive tool, but it wouldn't be able to completely replace what CSC is giving us.