How To Install snakemake on Kali Linux

In this tutorial we learn how to install snakemake on Kali Linux. snakemake is pythonic workflow management system

Introduction

In this tutorial we learn how to install snakemake on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove snakemake

Remove snakemake Configurations and Data

To remove snakemake configuration and data from Kali Linux 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

Summary

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