Installation of fastqc - MacOS Monterey - for command line

[NgugiJK]

Which is the appropriate file to download and install for MacOS Monterey? I have been trying to install via command line but not successful.

[s-andrews]

You have two options.

If you're wanting to run in an automated way - processing files on the command line rather than using a GUI then you want to use the same file as the linux install: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip

If you want to analyse files individually using a graphical interface then you'd be better to use the native mac app which is https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.dmg

In either case you'll need to install a suitable java runtime environment. We use the free ones from https://adoptium.net/ but any vaguely recent JRE should be fine.

If you're running the Mac application then make sure you read the part in the install notes about how to get past the security restrictions which OSX places on unsigned downloaded applications, as otherwise the app will be blocked.