How To Install vdjtools on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 425 words
Introduction
In this tutorial we learn how to install vdjtools on Ubuntu.
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 Ubuntu. 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 first since aptitude is usually not installed by default on Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove vdjtools
Remove vdjtools Configurations and Data
To remove vdjtools configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.