Setup and preparations

For this hands-on practical on processing genomics data for variant calling, we will make use of the same GitHub Codespaces that were introduced in 2  Setting up your own Unix shell.

Due to the large file size of the training data, not all files were included directly in the repository. When you launch your codespace for the first time (or whenever you create a new one), you will need to run the download scripts that are stored in ./training/data/, as described in the README.md.

If you want to follow along on your own machine instead, make sure to install all the required software tools. The easiest option is to use conda/mamba via the miniforge installer, and then installing all the packages described in the environment.yml file. For R, simply install the list of packages described in the devcontainer.json file (or renv file if it is available).

On Linux:

# download and install miniforge
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh

# install relevant packages into a new environment
mamba env create -n fimab -f ./FiMAB-bioinformatics/environment.yml

# activate environment
mamba activate fimab

On Windows: