How To Install ruby-rgfa on Ubuntu 18.04
Introduction
In this tutorial we learn how to install ruby-rgfa on Ubuntu 18.04.
What is ruby-rgfa
ruby-rgfa is:
The Graphical Fragment Assembly (GFA) format is a proposed file format to describe the product of a genome sequence assembly process. rgfa implements the proposed specifications for the GFA format described under https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md as closely as possible. The library allows one to create an RGFA object from a file in the GFA format or from scratch, to enumerate the graph elements (segments, links, containments, paths and header lines), to traverse the graph (by traversing all links outgoing from or incoming to a segment), to search for elements (e.g. which links connect two segments) and to manipulate the graph (e.g. to eliminate a link or a segment or to duplicate a segment distributing the read counts evenly on the copies).
There are three methods to install ruby-rgfa 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 ruby-rgfa Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ruby-rgfa using apt-get by running the following command:
sudo apt-get -y install ruby-rgfa
Install ruby-rgfa Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ruby-rgfa using apt by running the following command:
sudo apt -y install ruby-rgfa
Install ruby-rgfa 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 ruby-rgfa using aptitude by running the following command:
sudo aptitude -y install ruby-rgfa
How To Uninstall ruby-rgfa on Ubuntu 18.04
To uninstall only the ruby-rgfa package we can use the following command:
sudo apt-get remove ruby-rgfa
Uninstall ruby-rgfa And Its Dependencies
To uninstall ruby-rgfa and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove ruby-rgfa
Remove ruby-rgfa Configurations and Data
To remove ruby-rgfa configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge ruby-rgfa
Remove ruby-rgfa configuration, data, and all of its dependencies
We can use the following command to remove ruby-rgfa configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ruby-rgfa
References
Summary
In this tutorial we learn how to install ruby-rgfa package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
