How To Install qiime on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 483 words
Introduction
In this tutorial we learn how to install qiime on Ubuntu.
What is qiime
qiime is:
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:
- Integrated and automatic tracking of data provenance
- Semantic type system
- Plugin system for extending microbiome analysis functionality
- Support for multiple types of user interfaces (e.g. API, command line, graphical)
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
There are three methods to install qiime 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 qiime Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install qiime using apt-get by running the following command:
sudo apt-get -y install qiime
Install qiime Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install qiime using apt by running the following command:
sudo apt -y install qiime
Install qiime 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 qiime using aptitude by running the following command:
sudo aptitude -y install qiime
How To Uninstall qiime on Ubuntu
To uninstall only the qiime package we can use the following command:
sudo apt-get remove qiime
Uninstall qiime And Its Dependencies
To uninstall qiime and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove qiime
Remove qiime Configurations and Data
To remove qiime configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge qiime
Remove qiime configuration, data, and all of its dependencies
We can use the following command to remove qiime configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge qiime
Dependencies
qiime have the following dependencies:
References
Summary
In this tutorial we learn how to install qiime package on Ubuntu using different package management tools: apt, apt-get and aptitude.