How To Install python-biom-format on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-biom-format on Ubuntu 18.04.
What is python-biom-format
python-biom-format is:
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.
The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.
This package provides the BIOM format library for the Python 2 interpreter.
There are three methods to install python-biom-format 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 python-biom-format Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python-biom-format using apt-get by running the following command:
sudo apt-get -y install python-biom-format
Install python-biom-format Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-biom-format using apt by running the following command:
sudo apt -y install python-biom-format
Install python-biom-format 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 python-biom-format using aptitude by running the following command:
sudo aptitude -y install python-biom-format
How To Uninstall python-biom-format on Ubuntu 18.04
To uninstall only the python-biom-format package we can use the following command:
sudo apt-get remove python-biom-format
Uninstall python-biom-format And Its Dependencies
To uninstall python-biom-format and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-biom-format
Remove python-biom-format Configurations and Data
To remove python-biom-format configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-biom-format
Remove python-biom-format configuration, data, and all of its dependencies
We can use the following command to remove python-biom-format configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-biom-format
References
Summary
In this tutorial we learn how to install python-biom-format package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
