Installing Snakemake on Ubuntu (Linux)

Snakemake is a workflow management system to create scalable data analyses [1]. Workflows are defined in Python-based language. In this article, we are going to install Snakemake on Ubuntu (Linux).

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

Before installing Snakemake, you need to install Conda and Mamba. To install Conda, read this article.

Installing Mamba

In the terminal, paste the following command.

$ conda install mamba -n base -c conda-forge

It will take some time to finish.

Installing Snakemake

Paste the following commands in the terminal.

$ conda activate base

$ mamba create -c conda-forge -c bioconda -n snakemake snakemake

It will start downloading the required packages.

After a successful downloading and installation, paste the following command.

$ conda activate snakemake

Now check the installation by running the following command

$ snakemake --help

It should display usage.

References

1. Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., … & Köster, J. (2021). Sustainable data analysis with Snakemake. F1000Research, 10.