GWAS_manhattanplots command not found

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

Introduction

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

GWAS_manhattanplots: command not found

or when using sudo you get the following error message

sudo: GWAS_manhattanplots: command not found

Solutions to GWAS_manhattanplots: command not found

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

In Ubuntu GWAS_manhattanplots is provided by pique package.

pique is:

PIQUE is a software pipeline for performing genome wide association studies (GWAS). The main function of PIQUE is to provide ‘convenience’ wrappers that allow users to perform GWAS using the popular program EMMAX (Kang et al., 2010) without the need to be familiar with all of the software tools used to generate the required EMMAX input files. PIQUE will also perform a number of quality control steps prior to running EMMAX, ensuring that the various input data files are in the correct format. PIQUE proceeds in two main stages although there are multiple entry and exit points from which the pipeline can be run. The first stage consists of running the “pique-input” program, which can read genotype and phenotype information in several different formats and generates all the necessary input files required to run EMMAX. The second step in the pipeline uses the “pique-run” program to actually run EMMAX using the files generated by “pique-input” (or pre-existing user-supplied input files) to perform the GWAS and output the analysis summary files.

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

sudo apt-get -y install pique

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

You can also use apt command to install pique.

sudo apt -y install pique

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

sudo aptitude install pique

Summary

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