How To Install bedtools on Kali Linux

Introduction

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

What is bedtools

bedtools is:

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.

The groupBy utility is distributed in the filo package.

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

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

sudo apt-get update

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

sudo apt-get -y install bedtools

Install bedtools Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install bedtools

Install bedtools 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 bedtools using aptitude by running the following command:

sudo aptitude -y install bedtools

How To Uninstall bedtools on Kali Linux

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

sudo apt-get remove bedtools

Uninstall bedtools And Its Dependencies

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

sudo apt-get -y autoremove bedtools

Remove bedtools Configurations and Data

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

sudo apt-get -y purge bedtools

Remove bedtools configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge bedtools

Dependencies

bedtools have the following dependencies:

• libbz2-1.0
• libc6
• libgcc-s1
• liblzma5
• libstdc++6
• zlib1g

References

• bedtools website

Summary

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