Installing StaG-mwc

StaG-mwc depends on a number of individual tools, most prominently it requires Snakemake, which is used to manage the overall analysis workflow. In addition, another important component for the StaG-mwc framework is Conda, which is used to manage additional dependencies. This documentation assumes you already have git installed.

Install conda and Snakemake

The first two things you need to install are:

  1. Conda
  2. Snakemake

The recommended way to get started using StaG-mwc is to download and install Conda. A good starting point is a clean miniconda3 installation. Miniconda3 is quick to install and does not require administrator permissions. Please also consider setting up your environment for Bioconda.

After installing Conda and activating the base environment, install snakemake into your base environment:

(base)$ conda install -c bioconda -c conda-forge snakemake

These are the only external dependencies you need to install manually. The correct versions of any remaining dependencies will be automatically downloaded and installed when you run the workflow the first time.

Download the workflow code

Clone the StaG-mwc repository using git to get a copy of the workflow:

(base)$ git clone

This will clone the repo into a folder called stag-mwc inside your current working directory. You will manage all workflow-related business from inside this folder (i.e. configuring and running the workflow).

The intended way of working with StaG-mwc is that you download/clone a complete copy of the repository for each analysis you intend to make. That way, the local copy you have will remain after the analysis has been run, so you can go back and see exactly what was run, and how. This forms the basis of how Snakemake enables traceability and reproducibility.


You have now installed StaG-mwc.