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 updateAfter updating apt database, We can install bedtools using apt-get by running the following command:
sudo apt-get -y install bedtoolsInstall 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 bedtoolsInstall 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 updateAfter 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:
References
Summary
In this tutorial we learn how to install bedtools package on Kali Linux using different package management tools: apt, apt-get and aptitude.
