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nrminor / oneroof

Base-, Variant-, and Consensus-calling under One Proverbial Roof. Work in progress!
MIT License
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ARM compatibility #3

Open ajlail98 opened 4 months ago

ajlail98 commented 4 months ago

Currently the pipeline doesn't work with ARM, but it would be very helpful to be able to use this on Apple Silicon computers.

nrminor commented 4 months ago

Quick update on this @ajlail98:

So far, I've had poor luck getting the containerized version of the pipeline working because of some limitations to the emulator Docker uses to "pretend" that an ARM architecture is actually an x86 architecture. However! I did figure out a successful workaround through through a pixi shell, which you can reproduce with the following steps when you have a chance.

  1. Make sure pixi is installed with x86 instructions with: PIXI_ARCH=x86_64 curl -fsSL https://pixi.sh/install.sh | bash
  2. In the same folder as the oneroof project files (most importantly, pyproject.toml), run pixi shell. This will install all of the project's dependencies and launch a subshell in your terminal where those dependencies will be available.
  3. In that subshell, you can use your nextflow run command as per usual.

I'll keep working on getting Docker to work, but this slightly hackier approach should work for now!