How To Install cnvkit on Ubuntu 22.04

In this tutorial we learn how to install cnvkit on Ubuntu 22.04. cnvkit is Copy number variant detection from targeted DNA sequencing

Introduction

In this tutorial we learn how to install cnvkit on Ubuntu 22.04.

What is cnvkit

cnvkit is:

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

There are three methods to install cnvkit on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install cnvkit Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install cnvkit

Install cnvkit Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install cnvkit

Install cnvkit 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 cnvkit using aptitude by running the following command:

sudo aptitude -y install cnvkit

How To Uninstall cnvkit on Ubuntu 22.04

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

sudo apt-get remove cnvkit

Uninstall cnvkit And Its Dependencies

To uninstall cnvkit and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove cnvkit

Remove cnvkit Configurations and Data

To remove cnvkit configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge cnvkit

Remove cnvkit configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge cnvkit

References

Summary

In this tutorial we learn how to install cnvkit package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.