PLINK - Revision history

Tanthony@uab.edu: added category biostatistics

2012-04-04T15:32:03Z

added category biostatistics

← Older revision		Revision as of 15:32, 4 April 2012
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	machines and architectures.		machines and architectures.

	[[Category:Software]]		[[Category:Software]][[Category:Bio-statistics]]

Tanthony@uab.edu: added category software

2012-04-04T14:14:15Z

added category software

← Older revision		Revision as of 14:14, 4 April 2012
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	distributed processing environments to be constructed on heterogeneous		distributed processing environments to be constructed on heterogeneous
	machines and architectures.		machines and architectures.

			[[Category:Software]]

Tanthony@uab.edu: added links

2012-03-20T13:51:38Z

added links

← Older revision		Revision as of 13:51, 20 March 2012
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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.		[http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml 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 [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.		The PLINK web site also has a [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.

Tanthony@uab.edu at 15:03, 19 March 2012

2012-03-19T15:03:53Z

← Older revision		Revision as of 15:03, 19 March 2012
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	~~/share/apps/plink/1.06~~
	\|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.		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 [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.		The PLINK web site also has a [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.

Tanthony@uab.edu: created page with generic stub

2012-03-19T15:03:10Z

created page with generic stub

New page

{{Generic_stub}}

/share/apps/plink/1.06
|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 [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.

Please see this [http://pngu.mgh.harvard.edu/~purcell/plink/contact.shtml#cite page for PLINK citing instructions].

To load PLINK into your environment, use the following module command:
<pre>
module load plink/plink
</pre>

The following commands are available
* [http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml plink] - The plink executable is the primary binary for this software. Click [http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml here] for the command line reference.
* [http://pngu.mgh.harvard.edu/~purcell/plink/gplink.shtml 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:
<pre>
[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

</pre>

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:
<pre>
install.packages("Rserve")
</pre>
|-
|[http://www.csm.ornl.gov/pvm/pvm_home.html 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.