How To Install stacks on Kali Linux

In this tutorial we learn how to install stacks on Kali Linux. stacks is pipeline for building loci from short-read DNA sequences

Introduction

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

What is stacks

stacks is:

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Note that this package installs Stacks such that all commands must be run as: $ stacks

There are three methods to install stacks 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 stacks Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install stacks

Install stacks Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install stacks

Install stacks 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 stacks using aptitude by running the following command:

sudo aptitude -y install stacks

How To Uninstall stacks on Kali Linux

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

sudo apt-get remove stacks

Uninstall stacks And Its Dependencies

To uninstall stacks and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove stacks

Remove stacks Configurations and Data

To remove stacks configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge stacks

Remove stacks configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge stacks

Dependencies

stacks have the following dependencies:

References

Summary

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