How To Install biom-format-tools on Debian 9

Introduction

In this tutorial we learn how to install biom-format-tools on Debian 9.

What is biom-format-tools

biom-format-tools 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 command-line tools for the BIOM format Python package.

There are three methods to install biom-format-tools on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install biom-format-tools Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install biom-format-tools using apt-get by running the following command:

sudo apt-get -y install biom-format-tools

Install biom-format-tools Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install biom-format-tools using apt by running the following command:

sudo apt -y install biom-format-tools

Install biom-format-tools 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 biom-format-tools using aptitude by running the following command:

sudo aptitude -y install biom-format-tools

How To Uninstall biom-format-tools on Debian 9

To uninstall only the biom-format-tools package we can use the following command:

sudo apt-get remove biom-format-tools

Uninstall biom-format-tools And Its Dependencies

To uninstall biom-format-tools and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove biom-format-tools

Remove biom-format-tools Configurations and Data

To remove biom-format-tools configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge biom-format-tools

Remove biom-format-tools configuration, data, and all of its dependencies

We can use the following command to remove biom-format-tools configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge biom-format-tools

Dependencies

biom-format-tools have the following dependencies:

• python3-numpy

References

• biom-format-tools website

Summary

In this tutorial we learn how to install biom-format-tools package on Debian 9 using different package management tools: apt, apt-get and aptitude.