How To Install bio-eagle on Debian 9
Introduction
In this tutorial we learn how to install bio-eagle on Debian 9.
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 Debian 9. 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 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 bio-eagle using aptitude by running the following command:
sudo aptitude -y install bio-eagle
How To Uninstall bio-eagle on Debian 9
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 Debian 9, 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 Debian 9 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 Debian 9 using different package management tools: apt, apt-get and aptitude.