Installing PLINK on your Virtual Machine

PLINK is a popular and well-documented tool for the association and population-based linkage analyses for genome-wide association studies (GWAS). PLINK is typically used as a command-line tool. In this article, we will show you how to install PLINK 1.90 on a Linux Virtual Machine in the Aridhia DRE Workspace.

Installing PLINK on a Linux Virtual Machine

1. Download PLINK to your local machine.

From your web browser on your local machine (not in your virtual machine), go to the PLINK Releases page and download the latest stable Linux 64 bit release.

2. Upload PLINK to the Workspace

In the Aridhia DRE Workspace, if you don't have an uploads folder already, create a new one by going into the Files tab and pressing on New folder. Name your folder uploads.

Next, navigate to the Files tab and open your uploads folder. From here, press the Upload tab -> Upload files or data. Upload your PLINK *.zip file here.

3. Install PLINK

Connect to the Virtual Machine and open the terminal. Navigate to the uploads folder and unzip PLINK:

cd /files/uploads 
sudo unzip plink_linux_x86_64_20200616.zip -d plink_install

4. Make PLINK accessible from the command line

To make PLINK accessible from the command line anywhere in the file system, we need to copy the PLINK executable to the usr/local/bin directory, and make it executable:

cd plink_install
sudo cp plink /usr/local/bin
sudo chmod 755 /usr/local/bin/plink

Next, you need to add PLINK to PATH. To do this, run:

sudo nano ~/.bashrc

This will open the nano editor in the terminal. Scroll down to the bottom of the file and add the following line:

export PATH=/usr/local/bin:$PATH

Click Ctrl+S and Ctrl+X to save and exit the file.

5. Test the installation

To test the installation, restart the terminal and run:

plink

If PLINK was installed correctly, the command should produce an output similar to the screenshot below.