problems with Nirodents installation in Docker - Apple Silicon

Pomierny commented 4 months ago

What happened?

Hi after creating a docker image I am having such error:

(base) bartoszpomierny@MBPBP nirodents % docker run -it bartoszpomierny/fmriprep-rodents:dev Traceback (most recent call last): File "/opt/conda/bin/artsBrainExtraction", line 8, in sys.exit(main()) File "/src/nirodents/nirodents/cli/brainextraction.py", line 131, in main from ..workflows.brainextraction import init_rodent_brain_extraction_wf File "/src/nirodents/nirodents/workflows/brainextraction.py", line 17, in from niworkflows.interfaces.bids import DerivativesDataSink as _DDS ModuleNotFoundError: No module named 'niworkflows'

What command did you use?

docker run -it

What version of the software are you running?

latest

How are you running this software?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

gdevenyi commented 4 months ago

You should check if you're running an apple arm docker image or x86_64. Some packages probably don't exist for arm and so the docker container is broken. This is a common apple silicon problem

eilidhmacnicol commented 4 months ago

The dockerfile is in the old style; this needs updating anyway, but niworkflows is indeed missing from this version of the dockerfile

Pomierny commented 4 months ago

@gdevenyi yes - linux/arm64 image is set

nipreps / nirodents