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Software Installation

Before the workshop begins, you will need a working Conda/Mamba installation and a Snakemake environment on your local machine.

1. Install Miniforge (Conda + Mamba)

We recommend Miniforge, a minimal Conda installer that ships with the fast mamba solver pre-configured and defaults to the community conda-forge channel. If you already have Anaconda or Miniconda installed and mamba is available, you can skip this step.

Download the Miniforge3 Windows x86_64 installer (.exe). Run it and follow the prompts. When asked, select "Add Miniforge3 to my PATH" so that conda and mamba are available from your terminal.

We strongly recommend using the Windows Subsystem for Linux (WSL 2) terminal for this workshop, as Snakemake's cluster integration is designed for Linux environments. Once WSL is set up, install the Linux version of Miniforge inside your WSL terminal.

Download the installer matching your chip:

  • Apple Silicon (M-series): Miniforge3-MacOSX-arm64.sh
  • Intel: Miniforge3-MacOSX-x86_64.sh

Run it from your terminal: 

bash Miniforge3-MacOSX-*.sh
Follow the prompts and allow the installer to initialize Conda in your shell.

Download and run the Linux x86_64 installer: 

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh
Follow the prompts and allow the installer to initialize Conda.

Verify Your Conda Installation

Close and reopen your terminal, then run:

conda --version
mamba --version

You should see version numbers printed for both commands.

2. Create a Snakemake Conda Environment

Rather than installing Snakemake into your base environment, we will create a dedicated environment. This is best practice and avoids dependency conflicts.

This command also pre-installs all the bioinformatics tools used in the workshop examples (FastQC, fastp, STAR, featureCounts, MultiQC). This means every command in the workshop will work right away. Later, in the Reproducibility section, you will see how to assign each tool its own isolated, version-locked environment per rule, and why that is a better long-term approach than a single shared environment.

mamba create -n snakemake_workshop -c conda-forge -c bioconda \
    snakemake \
    fastqc=0.12.1 \
    fastp=0.23.4 \
    star=2.7.11a \
    subread=2.0.6 \
    multiqc=1.21

This may take 5–10 minutes

Conda needs to solve and download several large packages, including STAR. Grab a coffee.

conda activate snakemake_workshop

Verify Your Snakemake Installation

snakemake --version

You should see the Snakemake version number (e.g., 8.x.x or 9.x.x). If so, you are ready for the workshop!

Activate your environment first

Remember to run conda activate snakemake_workshop at the start of each new terminal session before working through the exercises.