vdjtools command not found

In this troubleshooting guide we learn how to fix vdjtools command not found error message

Introduction

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

vdjtools: command not found

or when using sudo you get the following error message

sudo: vdjtools: command not found

Solutions to vdjtools: command not found

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

In Ubuntu vdjtools is provided by vdjtools package.

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

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

sudo apt-get -y install vdjtools

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

You can also use apt command to install vdjtools.

sudo apt -y install vdjtools

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

sudo aptitude install vdjtools

Summary

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