PLINK ​

PLINK 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 with the following command:

bash
sudo apt install plink

And use the following executable:

bash
plink1 --noweb

Install PLINK 1.9 with the following commands:

Make sure you have your personal bin directory in place:

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

Download the latest binary release of PLINK 1.9:

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

Unpack the archive:

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

Remove archive:

bash
rm -v ~/bin/plink_linux_x86_64_20231211.zip

Test by printing the version:

bash
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 is a little more cumbersome as it is not available in Ubuntu's package repositories.

You can either use Conda to install Plink2 package or follow with binary release below.

To install package into your Conda environment use this command:

bash
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:

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

Download the latest binary release of PLINK 2:

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

Unzip the archive:

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

Remove archive:

bash
rm -v ~/bin/plink2_linux_x86_64_latest.zip

You can now use the following executable:

bash
plink2

Troubleshooting ​

Install unzip if missing:

bash
sudo apt install -y unzip