How To Install stacks on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 389 words
Introduction
In this tutorial we learn how to install stacks on Ubuntu.
What is stacks
stacks is:
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Note that this package installs Stacks such that all commands must be run as:
$ stacks
There are three methods to install stacks on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install stacks Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install stacks using apt-get by running the following command:
sudo apt-get -y install stacks
Install stacks Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install stacks using apt by running the following command:
sudo apt -y install stacks
Install stacks 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 stacks using aptitude by running the following command:
sudo aptitude -y install stacks
How To Uninstall stacks on Ubuntu
To uninstall only the stacks package we can use the following command:
sudo apt-get remove stacks
Uninstall stacks And Its Dependencies
To uninstall stacks and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove stacks
Remove stacks Configurations and Data
To remove stacks configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge stacks
Remove stacks configuration, data, and all of its dependencies
We can use the following command to remove stacks configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge stacks
Dependencies
stacks have the following dependencies:
References
Summary
In this tutorial we learn how to install stacks package on Ubuntu using different package management tools: apt, apt-get and aptitude.