GenDBWiki/DeveloperDocumentation/ToolIntegration

Integrating a new Tool into GenDB

Although the GenDB system already contains a number of standard bioinformatics tools that can be used for genome annotation, you may want to include your own tool (either for predicting regions or functions) or one of the many tools out there that are not yet incorporated in the current GenDB distribution. Since all standard tools like Glimmer or BLAST are implemented in their own special GENDB::DB::Tool subclasses (see the GenDB datamodel and API for details) incorporating a new tool would usually require modifications of the GenDB datamodel. In order to avoid such changes that usually have an impact on all active project databases (new classes with own attributes are stored in new SQL tables) we have introduced the class GENDB::DB::Tool::Generic that can be used to implement new tools without modifying the datamodel. Using this generic class, additional tools are not implemented in a GENDB::DB::DB_Server module but in a Perl module, usually located in the GENDB/Tools/ directory.