gfadiff command not found

Introduction

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

gfadiff: command not found

or when using sudo you get the following error message

sudo: gfadiff: command not found

Solutions to gfadiff: command not found

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

In Ubuntu gfadiff is provided by ruby-rgfa package.

ruby-rgfa is:

The Graphical Fragment Assembly (GFA) format is a proposed file format to describe the product of a genome sequence assembly process. rgfa implements the proposed specifications for the GFA format described under https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md as closely as possible. The library allows one to create an RGFA object from a file in the GFA format or from scratch, to enumerate the graph elements (segments, links, containments, paths and header lines), to traverse the graph (by traversing all links outgoing from or incoming to a segment), to search for elements (e.g. which links connect two segments) and to manipulate the graph (e.g. to eliminate a link or a segment or to duplicate a segment distributing the read counts evenly on the copies).

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

sudo apt-get -y install ruby-rgfa

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

You can also use apt command to install ruby-rgfa.

sudo apt -y install ruby-rgfa

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

sudo aptitude install ruby-rgfa

Summary

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