How To Install gemma on Ubuntu

Posted on April 1, 2023  (Last modified on May 20, 2023 )

3 minutes  • 525 words

Introduction

In this tutorial we learn how to install gemma on Ubuntu.

What is gemma

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.

There are three methods to install gemma on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install gemma Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install gemma using apt-get by running the following command:

sudo apt-get -y install gemma

Install gemma Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install gemma using apt by running the following command:

sudo apt -y install gemma

Install gemma Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install gemma using aptitude by running the following command:

sudo aptitude -y install gemma

How To Uninstall gemma on Ubuntu

To uninstall only the gemma package we can use the following command:

sudo apt-get remove gemma

Uninstall gemma And Its Dependencies

To uninstall gemma and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove gemma

Remove gemma Configurations and Data

To remove gemma configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge gemma

Remove gemma configuration, data, and all of its dependencies

We can use the following command to remove gemma configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge gemma

Dependencies

gemma have the following dependencies:

• libc6
• libgcc-s1
• libgsl27
• libopenblas0
• libstdc++6
• zlib1g

References

• gemma website

Summary

In this tutorial we learn how to install gemma package on Ubuntu using different package management tools: apt, apt-get and aptitude.