search

replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
39 stars 16 forks source link

Check for WSL support (Linux inside Windows) #127

Closed RaverJay closed 2 years ago

RaverJay commented 3 years ago

Have a user for this, and there might be some specific errors.

Maybe someone can find time to test.

replikation commented 3 years ago

Alright. I used wsl before. I know that wsl2 and docker with nextflow works fine if you are working inside the linux pathsystem (/mnt/wsl/). (E.g. dont open e.g. win10 desktop and try to start from there).

replikation commented 3 years ago

Install docker desktop and activate wsl2 Kernel for it. Most of the issues are docker not beeing able to mount paths. But if 3verytging including input files are within/wsl/ its fine and works (tried it with what the phage)

RaverJay commented 2 years ago

Just a FYI, using docker inside WSL2 worked for the user I talked about, and poreCov was successfully used in field with this setup =)

replikation commented 2 years ago

@RaverJay do we have s super short "TLDR" on how to set this up? we can add this to the readme for windows users.

RaverJay commented 2 years ago

I can ask her, but I think it was basically just install docker in WSL2 and done, but there might be some pitfalls