mlstdbNet installation

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 'mlstdbnet' subdirectory of the cgi-bin directory of your web server. Copy the 'lib' and 'Plugins' directories into this directory also. Make sure the mlstdbnet.pl file is readable and executable by the web server daemon:

    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 a temporary directory, allowing read and write access to apache, within the web root, e.g. /var/www/html/tmp. Set the path to the temporary directory in the mlstdbnet.conf file.
  7. Create an empty reference database 'refs' 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.
  8. Create an empty export logging database 'export_log' by using the export_log.sql script (setup directory) from within PostgreSQL.
  9. Use the online configurator 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. Make sure that the <system> tag of the XML file contains a 'webroot' attribute set to the relative webroot of your website, e.g. /neisseria.
  10. 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 the online configurator.
  11. Databases can be curated using the curate.pl script. Put the curate.pl script in a password protected directory (using apache .htaccess) of cgi-bin (e.g. /cgi-bin/private). Make sure there is a user in the user's table of the database with a username that matches the logged-in name with a status of 'curator'. Copy (or symlink) the database XML file to the directory containing the curate.pl script.
  12. Copy stylesheet.css to /WEBROOT/DBASE NAME/ (substitute appropriate values). Modify this to change the look and feel of the website. You can also include header.html and footer.html files in this directory - the contents of these files surround the output of the script and enable you to include logos and navigation links etc. The curation website can be similarly modified with the inclusion of curate_header.html and curate_footer.html files in this directory.

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mlstdbNet home
Database software
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Help

The user guide provides further information about using the software.

Download

mlstdbNet v2.0.2 (477 kb)

Installation

Required packages
Installation guide
Configuration tips

Example configuration file

XML

XML description of database attributes explained

Please contact Keith Jolley if you experience any problems installing and configuring mlstdbNet.