Genome Enhancer is a web-based search engine that finds clusters
of repeated motifs and displays their relationship to nearby genes.

To set up your own Genome Enhancer website, you need:

    Python 2.3 or higher
    MySQL 4 or higher
    MySQL support module for Python
    mxTextTools for Python
    BioPython 1.30 or higher
    Webware 0.8 or higher

The "site" directory contains the website files to be served by
Webware.  It also contains a subdirectory named "ge" that contains
the search engine code, which is invoked by the webpage modules.

The "tools" directory contains the scripts you need to download
genomes from NCBI and convert them into the format that the search
engine uses (a BioSQL database, plus plain ASCII files containing
the nucleotide sequences).

To set up Genome Enhancer:

    1.  Prepare a MySQL user account that the website will use.

    2.  Edit the file "site/ge/app.py" and set the MySQL host,
        username, and password to match the account you created.
        Also adjust the locations of cache directories if desired.

    3.  Run "make" in the site/ge directory to build the scanner.

    4.  Follow the instructions in the README file in the "tools"
        directory to load genome data into your database.

    5.  Set up Webware (follow the Webware documentation).
        Edit the application configuration file for WebKit (in
        Webware) to make the "site" directory its default context.

    6.  Start WebKit.


-- Ka-Ping Yee <ping@zesty.ca>, 2006-10-31
