How To Install bedtools on Debian 10

Learn how to install bedtools on Debian 10 with this tutorial. bedtools is suite of utilities for comparing genomic features

Introduction

In this tutorial we learn how to install bedtools on Debian 10.

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 Debian 10. 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 first since aptitude is usually not installed by default on Debian. 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 Debian 10

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 Debian 10, we can use the command below:

sudo apt-get -y autoremove bedtools

Remove bedtools Configurations and Data

To remove bedtools configuration and data from Debian 10 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:

References

Summary

In this tutorial we learn how to install bedtools package on Debian 10 using different package management tools: apt, apt-get and aptitude.