bamCoverage command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

bamCoverage: command not found

or when using sudo you get the following error message

sudo: bamCoverage: command not found

Solutions to bamCoverage: command not found

How To Fix bamCoverage: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bamCoverage is provided by python3-deeptools package.

python3-deeptools is:

Aiming for compatibility with the Galaxy worklfow environment, but also independently contributing to a series of workflows in genomics, this package provides a series of tools to address common tasks for the processing of high-throughput DNA/RNA sequencing.

To fix this problem, we can install more using the command below.

sudo apt-get -y install python3-deeptools

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install python3-deeptools.

sudo apt -y install python3-deeptools

Or if you have aptitude installed you can use the following command.

sudo aptitude install python3-deeptools

Summary

In this tutorial we learn how to fix bamCoverage command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.