Instructions for setting up mlstdbNet software

   1. Copy the distribution package to a temporary directory.

   2. Unpack the package using the following commands:

      gunzip mlstdbnet.tar.gz
      tar xvf mlstdbnet.tar

   3. Copy the mlstdbnet.pl script from the cgi-bin directory into a subdirectory of the cgi-bin directory of your web server. Make sure the file is readable and executable by everyone:

      chmod a+rx *

   4. Copy the java directory into the document root (e.g. /var/www/html/java).

   5. Copy the contents of the conf directory to /usr/local/mlstdbnet - this location can be changed by modifying the path to mlstdbnet.conf at the beginning of the mlstdbnet.pl script. Edit the mlstdbnet.conf file to suit your configuration - set the paths to any helper programs/modules installed or switch off functionality.

   6. Create an empty reference database by using the refs.sql script (setup directory) from within PostgreSQL. To populate the refs database, run the getrefs.pl script as a nightly cron job once isolate databases have been set up.

   7. Create an empty export logging database by using the export_log.sql script (setup directory) from within PostgreSQL.

   8. Use the dbConfig program to configure your MLST databases. This generates SQL files that can be used to create the databases from within PostgreSQL. The XML files produced should be copied to the appropriate cgi-bin directory.

   9. Create an HTML index page for your website. From the index page, link to the script entry page for the database, which is located at '/cgi-bin/mlstdbnet/mlstdbnet.pl?file=XMLFILE.xml' where XMLFILE.xml is the xml file created by dbConfig.

  10. Databases can be curated using the WDBI software. dbConfig creates the configuration files and a sample curation home page for the database.

  11. Use the mlstdbnet_genstats.pl script to generate a breakdown statistics page for the database - run this as a nightly cron job.

      mlstdbnet_genstats.pl <XMLFILE>
      The output for this file should be directed to
      /WEBROOT/DBASE NAME/stats.html (substitute appropriate values). 