How To Install vdjtools on Kali Linux

In this tutorial we learn how to install vdjtools on Kali Linux. vdjtools is framework for post-analysis of B/T cell repertoires

Introduction

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

What is vdjtools

vdjtools is:

VDJtools is an open-source Java/Groovy-based framework designed to facilitate analysis of immune repertoire sequencing (RepSeq) data. VDJtools computes a wide set of statistics and is able to perform various forms of cross-sample analysis. Both comprehensive tabular output and publication-ready plots are provided.

The main aims of the VDJtools Project are:

  • To ensure consistency between post-analysis methods and results
  • To save the time of bioinformaticians analyzing RepSeq data
  • To create an API framework facilitating development of new RepSeq analysis applications
  • To provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background

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

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

sudo apt-get update

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

sudo apt-get -y install vdjtools

Install vdjtools Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install vdjtools

Install vdjtools 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 vdjtools using aptitude by running the following command:

sudo aptitude -y install vdjtools

How To Uninstall vdjtools on Kali Linux

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

sudo apt-get remove vdjtools

Uninstall vdjtools And Its Dependencies

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

sudo apt-get -y autoremove vdjtools

Remove vdjtools Configurations and Data

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

sudo apt-get -y purge vdjtools

Remove vdjtools configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge vdjtools

Dependencies

vdjtools have the following dependencies:

References

Summary

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