Set Up Conda Environment¶

Platform¶

Choose your platform to get recommendations:

Linux

You should be able to install everything on Linux systems.

Windows

We recommend using the Windows Subsystem for Linux (WSL) for the best experience. If you are using WSL, please follow the instructions for Linux.

MacOS

You should be able to install everything on MacOS systems.

Note

All installation commands are intended for the Bash shell, which is the default on most macOS systems. If you use a different shell (like zsh), they should still work, but let us know if you have issues.

Set Up Conda Environment¶

We recommend to create and set up an empty conda environment:

conda create -n gadma_workshop_env python=3.10
conda activate gadma_workshop_env

Add channels that we are going to use for installations:

conda config --add channels bioconda
conda config --add channels conda-forge

BCFtools Installation¶

We will require bcftools that can be easily installed using conda:

conda install bcftools