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*     The Quick Start Guide to Setting Up and Running Genome Explorer     *
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1) make sure you have java 1.4 running on your system.
   open a command window and type "java -version" (no quotes) to see your current version.
   if the command 'java' is not found, download the jre from http://java.sun.com.

2) download and unzip bioPrograms.zip to the local hard drive on which you store programs.

3) download and unzip sample.zip to the local hard drive on which you store data.
   If you put it in a sub directory, enusure all outer directories have DOS COMPLIANT names.
   i.e. No spaces and less than 8 characters.
   Also ensure no files/directories are 'read only' 
	 (right click on the folder icon, select properties, uncheck 'read only').

4) edit the sample\param\genexpEnv.bat file (right click | edit) to reflect your directory
   structure.  There are 4 lines to edit.  Instructions are given above each line.

5) run (double click) sample\param\createGenExpInf.bat (to create an inf file that defaults to the 
   directories within the sample directory).
   
6) run (double click) genexp.bat to launch genome explorer.

-- OPTIONAL --
 
7) To create a shortcut to genome explorer on your desktop, right click on sample\param\genexp.bat 
   and drag it onto the desktop.  Select 'create shortcut here' from the list of options.
   
-- STRUCTURED TUTORIALS --

For a structured tutorial try following the user trial worksheets.
The worksheets and trial data are in the zip files blastTrial.zip, phyloTrial.zip and dianaTrial.zip.

Instructions for setting up the user trial environment variables are given in readme.txt within each zip file.