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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 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:
|- |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.