Honey.py command not found

Introduction

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

Honey.py: command not found

or when using sudo you get the following error message

sudo: Honey.py: command not found

Solutions to Honey.py: command not found

How To Fix Honey.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu Honey.py is provided by pbhoney package.

pbhoney is:

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

PBHoney is part of the PBSuite.

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

sudo apt-get -y install pbhoney

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

You can also use apt command to install pbhoney.

sudo apt -y install pbhoney

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

sudo aptitude install pbhoney

Summary

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