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Installing PLINK on your Virtual Desktop

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.

  1. Download PLINK to your local machine.
    From your web browser, go to the PLINK Releases page and download the latest stable Linux 64 bit release.
  2. Upload to Files. In the Aridhia DRE Workspace, if you don't have an uploads folder already, create a new one by going into the Add tab and pressing on New Folder. Name your folder uploads.
  3. Then navigate to the Files tab and open your uploads folder. From here, press Add tab -> Upload File. Upload your PLINK _*.zip_ file here.
  4. Install PLINK.
    Connect to the Virtual Desktop and open the terminal. First, change the directory: cd /files/uploads Unzip the file into a new folder: sudo unzip plink_linux_x86_64_20200616.zip -d plink_install
  5. Move PLINK executable
    To make PLINK accessible from the command line anywhere in the file system, we need to move PLINK executable to the usr/local/bin directory: cd /plink_install
    sudo cp plink /usr/local/bin
  6. Test the installation: cd ..
    If PLINK was installed correctly, the command should produce a similar output like the screenshot below.

If you get an error saying command 'plink' not found, then you need to add /usr/local/bin directory to path: sudo nano ~/.bashrc Here, 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. Restart the terminal and try running plink again.

Updated on December 9, 2020

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