GenDBWiki/CoreDocumentation/AdditionalScripts

Additional GenDB CORE Scripts

The following list contains some Perl scripts that were implemented for some general tasks involved in maintaining and working with the GenDB system. All scripts are developed and maintained by the GenDB core development team but before applying a script to your own projects you should always read the documentation and probably also have a look at the source code.

All scripts are used on your own risk, so have your backup prepared for the worst case!

The scripts are part of the GenDB distribution and thus located in the 'gendb/share/exec/' directory of your current GenDB environment. Execute all scripts from the 'gendb/bin/' directory using the 'gendb_start' wrapper script. Executing a script without any arguments gives a detailed usage message where all available options are explained.

• add_annotator.pl - This script can be used for adding a human annotator to a GenDB project database. Usually this is already done automatically by the GPMS whenever a new member is added to a project as an annotator.
• cleanup_database.pl - This script checks a number of GenDB objects for consistency. Objects with illegal references e.g. to already deleted objects are removed and deleted automatically.
• optimize_tables.pl - Use this script after larger database operations like computing several tools in order to optimize all tables automatically.
• set_user_config.pl - A default user configuration can be set for an existing GenDB user account with this script.