Issue with Mac M1 processor about workshop-snakemake-sibdays2022 HOT 4 OPEN

Hi Sebastien,

Thanks for reporting that. Do you have a list of dependencies missing for arm64? I know this architecture is making things complicated for containers at the moment, and I don't have a way to test it myself, but if you have a list we can make a specific environment file for that.

If you installed mamba in the base environment it should be accessible in the PATH (it will be in /path/to/miniconda/base/env/bin). It's working for me on Linux at least. If you have mamba installed in the base environment and it's not working then there's likely another issue

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Here is what I got

$ conda env create -f workshop.yaml 
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - bcftools=1.15.1
  - samtools=1.15.1
  - bwa=0.7.17

For me mamba is not in PATH both on Linux and Mac

from workshop-snakemake-sibdays2022.

This is pretty strange, I checked the bwa Conda recipe and there is no osx skip. It should be at least resolved regardless of the system.
My intuition is that if you are already routinely using conda, there might be some setup conflicts (default channels, channel order...). I would be happy to have a look with you today or tomorrow before the workshop if you want

from workshop-snakemake-sibdays2022.

We can have a look tomorrow. I can connect to a Linux desktop for the workshop.

I don't use conda. But I first installed it with brew. It may have cause some issues.

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