GenomeExplorer install readme, 09-Feb-03

To run GenomeExplorer on your PC:

1) install the Java Runtime Environment version 1.4.1.  Check the version from a 
   command prompt
   
   c:\> java -version

2) download genExp.jar, genExp.inf and gexExpDoc.zip from 
   http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html.
   To help with configuration, you can download defaultDirStructure.zip (a zip file
   of empty directories).
   
3) download biojava.jar, jakarta-regex.jar and xcerces.jar from the biojava website

4) put all of the above files into the same directory and then unzip genExpDoc.zip.

5) install the bioinformatics programs you want to be able to run:
    a) clustalw
    b) ncbi-blast
    c) phylip 3.6a
    d) treeview
    e) chromtree
   Links to these downloads sites are provided on GenomeExplorer download page.
    
6) double click the genExp.jar file, or choose to open using javaw.exe.  
   To run from the command line, cd to the directory containing genExp.jar and 
   then type 'java -jar genExp.jar'
   
   c:\> cd genomeExplorerDir
   c:\genomeExplorerDir> java -jar genExp.jar
   
   Sometime clustalw will crash for no reason.  If this is a problem for you, make a 
   batch file (call it genExp.bat) with the following lines (the first one is designed to
   fail, so don't worry if the tmp.i doesn't exist):
   
   c:\bioProgramsDir\clustalw.exe -infile tmp.i
   java -jar c:\genomeExplorerDir\genExp.jar
   
   NB - you will need to ensure the paths are set correctly for your system.
 
7) choose 'settings' -> 'directories and executables...' to enter the paths to your installed
   bioinformatics programs, and default input and output directories.
   These settings are stored in the genExp.inf file.  This file can be edited in a text editor
   if desired.  If you downloaded defaultDirStructure.zip, it will be easier to do a 
   'search-and-replace' in a text editor.
   The documentation in unzipped from the genExpDoc.zip file will be available from within 
   genomeExplorer if you set the 'genome explorer documentation directory' path to point to 
   its directory.
   (This documentation needs to be updated for some programs, but should be still help 
   in its current state.)
   
GenomeExplorer should now run smoothly.  If it doesn't, email me with you problems and
I'll try to help you out.

jenn.conn@bbsrc.ac.uk.

p.s. GenomeExplorer is still under development.  A more polished versions should be 
available shortly.