Starting Snakemake

The workshop slides are available here: Supercharge Your Analyses with Snakemake

This repository provides a simple multi-folder tutorial:

1. 01_jupyter – Jupyter-based example that fetches Wikipedia data and plots a histogram.
2. 02_simple_snakemake – Minimal Snakefile demonstrating a single rule.
3. 03_wildcards – More complex pipeline that processes multiple links and combines results.

Installation

To install snakemake and the dependencies for jupyter and matplotlib:

hostname
# della8.princeton.edu
module load anaconda3/2024.6
conda create -n snake -y
conda activate snake
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
conda install snakemake jupyterlab matplotlib -y
snakemake --version
# 8.28.0

We will use the snake environment for the rest of the material.