PLINK

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 http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml for instructions. You'll need to install the Rserve package to use the plugin, for example: install.packages("Rserve") distributed processing environments to be constructed on heterogeneous machines and architectures.
 * pvm
 * 3.4.5
 * /usr/bin/pvm
 * PVM3 (Parallel Virtual Machine) is a library and daemon that allows
 * PVM3 (Parallel Virtual Machine) is a library and daemon that allows