About

What I consider to be the best currently available software stack for bioinformatics and data science.

Requirements

• nix package manager
• git

Environment setup

1. Clone the repo and run nix shell
   • This will install positron and pixi
2. Pixi:
   • use pixi install to install all the dependencies
   • if on windows use pixi run setup-r-packages to install R specific dependencies unavailable on conda
   • make sure to run pixi shell, otherwise positron will not be able to see the shell
3. Positron:
   • start using positron . in working pixi directory
   • in settings enable R pixi environment detection
   • in settings disable `use bundled ipykernel"
   • works with system installation too! (flake based positron install not necessary)
4. Enable direnv