How To Install hyphy-pt on Ubuntu 18.04
Introduction
In this tutorial we learn how to install hyphy-pt on Ubuntu 18.04.
What is hyphy-pt
hyphy-pt is:
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.
This package provides an executable using pthreads to do multiprocessing.
There are three methods to install hyphy-pt on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install hyphy-pt Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install hyphy-pt using apt-get by running the following command:
sudo apt-get -y install hyphy-pt
Install hyphy-pt Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install hyphy-pt using apt by running the following command:
sudo apt -y install hyphy-pt
Install hyphy-pt 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 hyphy-pt using aptitude by running the following command:
sudo aptitude -y install hyphy-pt
How To Uninstall hyphy-pt on Ubuntu 18.04
To uninstall only the hyphy-pt package we can use the following command:
sudo apt-get remove hyphy-pt
Uninstall hyphy-pt And Its Dependencies
To uninstall hyphy-pt and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove hyphy-pt
Remove hyphy-pt Configurations and Data
To remove hyphy-pt configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge hyphy-pt
Remove hyphy-pt configuration, data, and all of its dependencies
We can use the following command to remove hyphy-pt configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge hyphy-pt
References
Summary
In this tutorial we learn how to install hyphy-pt package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
