PLINK
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
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The Research Computing Team
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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:
install.packages("Rserve")
|- |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.