Setup - Required software not available for osx-arm64

[clarajegousse]

Hello,

Just wanted to point out that bwa and BCFtools are not available through bioconda for osx-arm64.

A possible workaround is to use brew to install these two pieces of software

brew install bwa
brew install bcftools

More info:
https://formulae.brew.sh/formula/bwa
https://formulae.brew.sh/formula/bcftools

Let me know if you would like me to make a pull request about this :)

[MarieHouillon]

Hello,

We've just run the workshop, and indeed, the setup instructions for macOS need to be updated:

• The link to the Miniconda installer is for x86_64, the arm64 installer could be added.
• bwa version 0.7.17 is not compatible with arm64. Maybe 0.7.18 could be used instead?
• Due to a version incompatibility with zlib, I was unable to install samtools and bcftools via conda.
• This is a more general issue, but when bcftools is installed via homebrew (or from sources), vcfutils.pl is not in the PATH by default. For Homebrew installation, it is in /opt/homebrew/Cellar/bcftools/1.21/bin but not in /opt/homebrew/bin. When compiling from sources, it is in bcftools-1.9/misc.

Also, we cannot control which version is installed when using Homebrew. I guess this is an issue?

I will try to propose a pull request soon.

[twrightsman]

@MarieHouillon As I don't use or have access to macOS I would greatly appreciate a pull request. Thank you for looking into this!