biom command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
biom: command not found
or when using sudo you get the following error message
sudo: biom: command not found
Solutions to biom: command not found
How To Fix biom: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu biom is provided by python3-biom-format package.
python3-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 3 interpreter.
To fix this problem, we can install more using the command below.
sudo apt-get -y install python3-biom-format
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install python3-biom-format.
sudo apt -y install python3-biom-format
Or if you have aptitude installed you can use the following command.
sudo aptitude install python3-biom-format
Summary
In this tutorial we learn how to fix biom command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.