olouant/enccb-workflow-snakemake

Repository for Snakemake session of the HPC Workflow @ENCCB training 15-16 Feb. 2022

HPC Workflow training @ENCCB - Snakemake

This repository contains the material used for the Snakemake session of the HPC Workflow @ENCCB training delivered 15-16th February 2022.

Useful Links

• Snakemake Documentation
• Installing Snakemake

Launch the Demo Notebook on Binder

You can launch the demo Jupyter Notebook used to introduce Snakemake on Binder by using this link.

Launch the Demo on your Own Computer

You can launch MacOS, Linux or Windows subsystem for Linux

git clone https://github.com/olouant/enccb-workflow-snakemake.git && \
cd enccb-workflow-snakemake

Assuming you have Python 3 installed on your machine, create a virtual environment, activate it and install the required dependencies.

python3 -m venv demoenv && \
source ./demoenv/bin/activate && \
pip install -r ./envs/requirements.txt

Then you can launch Jupyter Lab and open the URL provided in the output in your browser

jupyter lab

Note the dot command provided by Graphviz is required to generate the DAG images. See here to see how to install this tool for your OS.