Introduction
In this tutorial we learn how to install beagle on Ubuntu 22.04.
What is beagle
beagle is:
Beagle performs genotype calling, genotype phasing, imputation of ungenotyped
markers, and identity-by-descent segment detection. Genotypic imputation works
on phased haplotypes using a Li and Stephens haplotype frequency model.
Beagle also implements the Refined IBD algorithm for detecting
homozygosity-by-descent (HBD) and identity-by-descent (IBD) segments.
There are three methods to install beagle 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 beagle Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install beagle using apt-get by running the following command:
sudo apt-get -y install beagle
Install beagle Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install beagle using apt by running the following command:
sudo apt -y install beagle
Install beagle 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 beagle using aptitude by running the following command:
sudo aptitude -y install beagle
How To Uninstall beagle on Ubuntu 22.04
To uninstall only the beagle package we can use the following command:
sudo apt-get remove beagle
Uninstall beagle And Its Dependencies
To uninstall beagle and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove beagle
Remove beagle Configurations and Data
To remove beagle configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge beagle
Remove beagle configuration, data, and all of its dependencies
We can use the following command to remove beagle configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge beagle
References
Summary
In this tutorial we learn how to install beagle package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
