Initial Setup

Clone the repository:

git clone git@github.com:trafalmadorian97/mecfs_bioinformatics.git

We use Pixi as are our package manager. Setup Pixi as described here, using the bash command:

curl -fsSL https://pixi.sh/install.sh | sh

After setup, source your bashrc to make sure pixi is on your path:

source ~/.bashrc

To verify everything is working correctly, try:

pixi r invoke init

This will install additional required packages, then run linters and tests.

A natural next step is to run the basic analysis of the Decode ME data using the script here.

You can use pixi to run this or another script via the command:

pixi r python [PATH_TO_SCRIPT]