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

The PLINK web site also has a tutorial section that users should read through.

Please see this page for PLINK citing instructions.

To load PLINK into your environment, use the following module command:

module load plink/plink

The following commands are available

  • plink - The plink executable is the primary binary for this software. Click here for the command line reference.
  • gplink - This is a java based GUI for PLINK that provides the following functionality:
    • is a GUI that allows construction of many common PLINK operations
    • provides a simple project management tool and analysis log
    • allows for data and computation to be on a separate server (via SSH)
    • facilitates integration with Haploview

Running gplink: You should NOT run gplink from the cheaha login node (head node), only from the compute nodes using the qrsh command. The qrsh command will provide a shell on a compute node complete with X forwarding. For example:

[jsmith@cheaha ~]$ qrsh

Rocks Compute Node
Rocks 5.1 (V.I)
Profile built 13:06 21-Nov-2008

Kickstarted 13:13 21-Nov-2008

[jsmith@compute-0-10 ~]$ module load plink/plink

[jsmith@compute-0-10 ~]$ gplink

You should see the gPLINK window open. If you get an error similar to "No X11 DISPLAY variable was set", make sure your initial connection to Cheaha had X forwarding enabled.

If you want to use the PLINK R plugin functionality, please see this page for instructions. You'll need to install the Rserve package to use the plugin, for example:


|- |pvm |3.4.5 |/usr/bin/pvm |PVM3 (Parallel Virtual Machine) is a library and daemon that allows distributed processing environments to be constructed on heterogeneous machines and architectures.

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