Difference between revisions of "LocusZoom Standalone"
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== Requirements == | == Requirements == | ||
| − | + | The following software is required: | |
* [http://www.python.org/download/ Python 2.6] (do '''not''' download the 3.0 branch!) | * [http://www.python.org/download/ Python 2.6] (do '''not''' download the 3.0 branch!) | ||
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* [[New_Fugue|new_fugue]], a program for computing LD, written by Goncalo Abecasis. | * [[New_Fugue|new_fugue]], a program for computing LD, written by Goncalo Abecasis. | ||
| − | Currently only Unix/Linux is supported, though Mac OS X should be supported in a future release. | + | Currently only '''Unix/Linux''' is supported, though Mac OS X should be supported in a future release. |
== Synopsis == | == Synopsis == | ||
| Line 27: | Line 27: | ||
== Installation == | == Installation == | ||
| + | === Step 1: Install Python === | ||
| + | You will need to install Python on your system if it is already. Head over to [http://www.python.org www.python.org] to download it. Note that you will want to make sure to download the latest from the 2.x branch, and '''not''' the 3.0 one. | ||
| + | |||
| + | === Step 2: Install R === | ||
| + | R is also required for generating the plots. You can download R at [http://www.r-project.org/ www.r-project.org]. Version 2.10 or greater is required. | ||
| + | |||
| + | |||
== Configuration == | == Configuration == | ||
Revision as of 14:44, 24 May 2010
This page contains information regarding a version of LocusZoom that may be downloaded for personal use. For more information on LocusZoom, see this page.
Requirements
The following software is required:
- Python 2.6 (do not download the 3.0 branch!)
- R 2.10+
- new_fugue, a program for computing LD, written by Goncalo Abecasis.
Currently only Unix/Linux is supported, though Mac OS X should be supported in a future release.
Synopsis
A quick example
First, change directory into examples/. Then, run the following command:
./run_example.py
This script runs the following command for you:
../bin/locuszoom --metal Kathiresan_2009_HDL.txt --refgene FADS1
A PDF plot of the FADS1 locus will be created in the directory. Voila, your first region plot!
Installation
Step 1: Install Python
You will need to install Python on your system if it is already. Head over to www.python.org to download it. Note that you will want to make sure to download the latest from the 2.x branch, and not the 3.0 one.
Step 2: Install R
R is also required for generating the plots. You can download R at www.r-project.org. Version 2.10 or greater is required.
