How To Install parsnp on Ubuntu 22.04
Introduction
In this tutorial we learn how to install parsnp on Ubuntu 22.04.
What is parsnp
parsnp is:
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
There are three methods to install parsnp on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install parsnp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install parsnp using apt-get by running the following command:
sudo apt-get -y install parsnp
Install parsnp Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install parsnp using apt by running the following command:
sudo apt -y install parsnp
Install parsnp 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 parsnp using aptitude by running the following command:
sudo aptitude -y install parsnp
How To Uninstall parsnp on Ubuntu 22.04
To uninstall only the parsnp package we can use the following command:
sudo apt-get remove parsnp
Uninstall parsnp And Its Dependencies
To uninstall parsnp and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove parsnp
Remove parsnp Configurations and Data
To remove parsnp configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge parsnp
Remove parsnp configuration, data, and all of its dependencies
We can use the following command to remove parsnp configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge parsnp
References
Summary
In this tutorial we learn how to install parsnp package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
