gmap_build command not found

In this troubleshooting guide we learn how to fix gmap_build command not found error message

Introduction

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

gmap_build: command not found

or when using sudo you get the following error message

sudo: gmap_build: command not found

Solutions to gmap_build: command not found

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

In Ubuntu gmap_build is provided by gmap package.

gmap is:

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

  • known splice sites and identify novel splice sites.
  • known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

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

sudo apt-get -y install gmap

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

You can also use apt command to install gmap.

sudo apt -y install gmap

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

sudo aptitude install gmap

Summary

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