Hi folks < David Lecomber> and I are poking around in this p nf-core #spatialvi

Hi folks - <@U07RHAG6D89> and I are poking around ...

Phil Ewels

03/11/2025, 9:20 AM

Hi folks - @David Lecomber and I are poking around in this pipeline trying to get linux/arm64 support running (see the #C07S9BW2STT channel). I was wondering what env/environment.yml file is used for? It struck me that it looks quite a lot like the shared

nf-core/quartonotebook

module (with its own environment file). Is it possible that the former is a historical relic and not used anywhere? Or have I just missed where it is?

Erik Fasterius

03/12/2025, 7:59 AM

The Conda environment file is what's used to install things inside the Docker container (which is also done in the

quartonotebook

module). The installation for the packages that are used in the pipeline is, sadly, non-trivial, so this was the solution that has worked so far. We haven't checked recently if it's possible to install using e.g. Seqera Containers, but that's something that we will check once the active development on implementing Visium HD into the pipeline is finished (as that requires additional changes to the environment).

Erik Fasterius

03/12/2025, 8:09 AM

Also, the image currently used is a multi-platform image for linux/amd64 and linux/arm64, so that part is at least already working.

Phil Ewels

03/12/2025, 8:15 AM

Which parts of the pipeline use this container, and what's it called?

Phil Ewels

03/12/2025, 8:16 AM

Is it the two local modules you're talking about?

Phil Ewels

03/12/2025, 8:17 AM

So the read data and merge data scripts, using docker.io/erikfas/spatialvi ?

Erik Fasterius

03/12/2025, 8:29 AM

It's currently three separate modules (which could possibly be divided up further once the environment is finalised, but there might still be quite some overlap so one reason to keep it reused for all relevant modules):

read_data

merge_data

and

quartonotebook

Phil Ewels

03/12/2025, 10:09 AM

gotcha, ok this was super helpful, thanks

Phil Ewels

03/12/2025, 10:09 AM

If you get a moment, would you mind adding a bunch of comments into these files so that when I stumble across them again in six months and have inevitably forgotten this conversation, it'll be obvious to someone reading?

Phil Ewels

03/12/2025, 10:10 AM

eg. both of the

env/

files saying that these are used to create the image xxx which is used in processes yyyy

Phil Ewels

03/12/2025, 10:10 AM

And again in the process code, next to the container - saying where the environment and docker files are

Phil Ewels

03/12/2025, 10:11 AM

I also wonder if it'd make sense to remove the

Dockerfile

and

environment,yml

file from the quartonotebook module if they're not being used? That threw me a bit (should be fine to do with

nf-core modules patch

I think?)

Phil Ewels

03/12/2025, 10:11 AM

And finally,

<http://docker.io/erikfas/spatialvi|docker.io/erikfas/spatialvi>

should really be switched over to

<http://quay.io/nf-core/spatialvi|quay.io/nf-core/spatialvi>

at some point - though I understand that if it's still in heavy flux right now then it might not be convenient to do so (as it needs someone from the core team to push updates)

Phil Ewels

03/12/2025, 10:12 AM

Again if you add a comment next to it saying that this will be pushed there in the future, that'll stop me / other people asking about it again 😅

Erik Fasterius

03/12/2025, 11:35 AM

Sure, I can add some comments, no worries! Yes, we can also remove the module environment with a patch, good point.

Phil Ewels

03/12/2025, 1:45 PM

Thank you! 🙏🏻

Open in Slack

Previous Next