How To Install bedtools on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 388 words
Introduction
In this tutorial we learn how to install bedtools on Ubuntu.
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 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 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 Ubuntu. 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 Ubuntu
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 Ubuntu, we can use the command below:
sudo apt-get -y autoremove bedtools
Remove bedtools Configurations and Data
To remove bedtools configuration and data from Ubuntu 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 Ubuntu using different package management tools: apt, apt-get and aptitude.