How To Install bio-eagle on Kali Linux

In this tutorial we learn how to install bio-eagle on Kali Linux. bio-eagle is Haplotype phasing within a genotyped cohort or using a phased reference panel

Introduction

In this tutorial we learn how to install bio-eagle on Kali Linux.

What is bio-eagle

bio-eagle is:

Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. The basic idea of the Eagle1 algorithm is to harness identity-by-descent among distant relatives??which is pervasive at very large sample sizes but rare among smaller numbers of samples??to rapidly call phase using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Please note: The executable was renamed to bio-eagle because of a name clash. Please read more about this in /usr/share/doc/bio-eagle/README.Debian.

There are three methods to install bio-eagle 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 bio-eagle Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install bio-eagle

Install bio-eagle Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install bio-eagle

Install bio-eagle 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 bio-eagle using aptitude by running the following command:

sudo aptitude -y install bio-eagle

How To Uninstall bio-eagle on Kali Linux

To uninstall only the bio-eagle package we can use the following command:

sudo apt-get remove bio-eagle

Uninstall bio-eagle And Its Dependencies

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

sudo apt-get -y autoremove bio-eagle

Remove bio-eagle Configurations and Data

To remove bio-eagle configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge bio-eagle

Remove bio-eagle configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge bio-eagle

Dependencies

bio-eagle have the following dependencies:

References

Summary

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