How To Install gubbins on Debian 10
Introduction
In this tutorial we learn how to install gubbins on Debian 10.
What is gubbins
gubbins is:
Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
There are three methods to install gubbins on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install gubbins Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install gubbins using apt-get by running the following command:
sudo apt-get -y install gubbins
Install gubbins Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install gubbins using apt by running the following command:
sudo apt -y install gubbins
Install gubbins 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 gubbins using aptitude by running the following command:
sudo aptitude -y install gubbins
How To Uninstall gubbins on Debian 10
To uninstall only the gubbins package we can use the following command:
sudo apt-get remove gubbins
Uninstall gubbins And Its Dependencies
To uninstall gubbins and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove gubbins
Remove gubbins Configurations and Data
To remove gubbins configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge gubbins
Remove gubbins configuration, data, and all of its dependencies
We can use the following command to remove gubbins configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge gubbins
Dependencies
gubbins have the following dependencies:
References
Summary
In this tutorial we learn how to install gubbins package on Debian 10 using different package management tools: apt, apt-get and aptitude.