WGAViewer

Installation

The WGAViewer package comes in one ZIP file, or a Windows installation package (.exe file).

[1] LINUX/UNIX/MAC users should use the ZIP package. Unzip (extract) this file to a folder. No additional installation is necessary. The ZIP file has to be unzipped to run the program. WGAViewer cannot be launched from a ZIP folder (for example, opened by Windows explorer).

[2] For Windows installation package, simply double-click the .exe file and follow the instructions. There are some specific notes for "Windows vista" user below.

The size of the full functional release is about 180MB. A “Lite” version is also offered for downloading with a reduced size of around 40MB. Without the support database for selection and GENEVAR, this “Lite” version can perform genic and LD annotation but not annotations for gene expression or selection.

Starting the program

[1] Windows users should double click “WGAViewer.exe” in the home folder to launch the program.

[2] For LINUX/UNIX/MAC users, there is a “WGAViewer.sh” in the home folder. Change the permission of this file to be runnable, for example by typing: “chmod +x WGAViewer.sh” in the terminal window. And then double click this file to launch the program.

Alternatively, double click a jar file in the home folder: WGAViewer.jar. to start the program, or type “java -jar WGAViewer.jar” in a terminal window.

An important note on memory issues

Check here for some tips on allocating enough memory to the annotation tasks, and solving potential memory-related problems.

An important note for LINUX/UNIX users:

By default, WGAViewer calls a command "htmlview" to start the web browser when navigating to online resources. This command can be changed through a configuration file in the WGAViewer home folder: "./configuration/internet.txt". Here is an example:

[Linux Internet]=htmlview

If the command for starting the web browser is different in your computer, simply change the 'htmlview' text accordingly in this file.

Important notes for Windows Vista users:

Windows Vista uses a rather different system management than other versions of Windows. To successfully run the WGAViewer program on a Windows Vista platform, we generally recommend these procedures:

[A] Do NOT use the Windows .exe installation package. Instead, use the ZIP package. Unzip (extract) this file to a folder that you have a full 'write' access to, for example, by creating a folder like "C:\WGAViewer".

[B] Check your system virtual memory (paging file size) settings. To access this information, right click on 'My Computer' to access 'System properties' -> 'Advanced' tab -> 'Performance' section, click on 'settings' button -> 'Advanced ' tab -> 'Virtual memory' section. If your 'Total paging file size' is less than 2048MB, we recommend to change this number to at least 2048MB. To do this, click on 'Change' button, select 'Custom size', and then type in '2048' as the initial size, and '5000' as the maximum size.

This setting allows the computer to use hard disk as 'virtual memory' when it runs out of 'physical memory'. Sometimes the Vista comes with a "0" virtual memory. For the case of the WGAViewer program, which usually uses a large amount of memory to load a GWAS dataset, a "0" virtual memory will sometimes cause a crash of the loading process, because of the memory shortage.