# PLINK

PLINK (opens new window) is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Install PLINK 1 (opens new window) with the following command:

sudo apt install plink

And use the following executable:

plink1 --noweb

Install PLINK 1.9 (opens new window) with the following commands:

Make sure you have your personal bin directory in place:

mkdir -p ~/bin && source ~/.profile

Download the latest binary release of PLINK 1.9:

wget -P ~/bin/ https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20231211.zip

Unpack the archive:

unzip  ~/bin/plink_linux_x86_64_20231211.zip -d ~/bin/

Remove archive:

rm -v ~/bin/plink_linux_x86_64_20231211.zip

Test by printing the version:

plink --version

You can also install PLINK 1.9 with Bioconda. See our Anaconda and Bioconda tutorial for more details.

# Using conda

Installing PLINK 2 (opens new window) is a little more cumbersome as it is not available in Ubuntu's package repositories.

You can either use Conda to install Plink2 package (opens new window) or follow with binary release below.

To install package into your Conda environment use this command:

conda install -c bioconda plink2

# Using binary release

To download and unpack the binary for PLINK 2 follow these steps.

Make sure you have your personal bin directory in place:

mkdir -p ~/bin && source ~/.profile

Download the latest binary release of PLINK 2:

wget -P ~/bin/ http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_latest.zip

Unzip the archive:

unzip ~/bin/plink2_linux_x86_64_latest.zip -d ~/bin/

Remove archive:

rm -v ~/bin/plink2_linux_x86_64_latest.zip

You can now use the following executable:

plink2

# Troubleshooting

Install unzip if missing:

sudo apt install -y unzip
Last Updated: 6/17/2024