smartpca command not found

Introduction

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

smartpca: command not found

or when using sudo you get the following error message

sudo: smartpca: command not found

Solutions to smartpca: command not found

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

In Ubuntu smartpca is provided by eigensoft package.

eigensoft is:

The EIGENSOFT package combines functionality from the group’s population genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

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

sudo apt-get -y install eigensoft

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

You can also use apt command to install eigensoft.

sudo apt -y install eigensoft

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

sudo aptitude install eigensoft

Summary

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