How To Install snakemake on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

2 minutes • 389 words

Introduction

In this tutorial we learn how to install snakemake on Ubuntu.

What is `snakemake`

snakemake is:

Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific language (DSL) in Python style, together with a fast and comfortable execution environment.

There are three methods to install snakemake on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install snakemake Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install snakemake using apt-get by running the following command:

sudo apt-get -y install snakemake

Install snakemake Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install snakemake using apt by running the following command:

sudo apt -y install snakemake

Install snakemake Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install snakemake using aptitude by running the following command:

sudo aptitude -y install snakemake

How To Uninstall snakemake on Ubuntu

To uninstall only the snakemake package we can use the following command:

sudo apt-get remove snakemake

Uninstall snakemake And Its Dependencies

To uninstall snakemake and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove snakemake

Remove snakemake Configurations and Data

To remove snakemake configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge snakemake

Remove snakemake configuration, data, and all of its dependencies

We can use the following command to remove snakemake configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge snakemake

Dependencies

snakemake have the following dependencies:

References

snakemake website

Summary

In this tutorial we learn how to install snakemake package on Ubuntu using different package management tools: apt, apt-get and aptitude.