snakemake command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

snakemake: command not found

or when using sudo you get the following error message

sudo: snakemake: command not found

Solutions to snakemake: command not found

How To Fix snakemake: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu snakemake is provided by snakemake package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install snakemake

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install snakemake.

sudo apt -y install snakemake

Or if you have aptitude installed you can use the following command.

sudo aptitude install snakemake

Summary

In this tutorial we learn how to fix snakemake command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.