gemma command not found

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

Introduction

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

gemma: command not found

or when using sudo you get the following error message

sudo: gemma: command not found

Solutions to gemma: command not found

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

In Ubuntu gemma is provided by gemma package.

gemma is:

GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS):

  • It fits a univariate linear mixed model (LMM) for marker association tests with a single phenotype to account for population stratification and sample structure, and for estimating the proportion of variance in phenotypes explained (PVE) by typed genotypes (i.e. “chip heritability”).
  • It fits a multivariate linear mixed model (mvLMM) for testing marker associations with multiple phenotypes simultaneously while controlling for population stratification, and for estimating genetic correlations among complex phenotypes.
  • It fits a Bayesian sparse linear mixed model (BSLMM) using Markov chain Monte Carlo (MCMC) for estimating PVE by typed genotypes, predicting phenotypes, and identifying associated markers by jointly modeling all markers while controlling for population structure.
  • It estimates variance component/chip heritability, and partitions it by different SNP functional categories. In particular, it uses HE regression or REML AI algorithm to estimate variance components when individual-level data are available. It uses MQS to estimate variance components when only summary statisics are available.

GEMMA is computationally efficient for large scale GWAS and uses freely available open-source numerical libraries.

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

sudo apt-get -y install gemma

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

You can also use apt command to install gemma.

sudo apt -y install gemma

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

sudo aptitude install gemma

Summary

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