OBSOLETE: Tripal GBrowse

This module provides an interface to register already existing GBrowse instances with Drupal/Tripal and/or create new GBrowse Instances. Furthermore, it allows basic management of these GBrowse instances including un-registering and/or deleting and loading of features in Tripal/Chado into a MySQL GBrowse instance. As such, it provides interoperability and syncronization between a Tripal/Chado installation and GBrowse.

Features of this Module:

• Register GBrowse Instance: In order to load features into a GBrowse instance you need to first register it with Tripal/Drupal. Any existing GBrowse instance that utilizes a MySQL database can be registered with the module. Furthermore, you can create new GBrowse Instances through this module by selecting that option in the register GBrowse Instance form. Thisnewly created GBrowse instance uses a MySQL database with is created and a user name and password is setup and a default configuration file is created. Finally, the database is initialized and the first sequence set is loaded into the GBrowse instance.
• Un-Register/Delete GBrowse Instance: Un-registering a GBrowse instance alone will remove the GBrowse instance from the Drupal site.When removing the entire instance, the database and the configuration file will be deleted. This cannot be undone!
• Load Feature (Libraries) Libraries: Simply by selecting a Tripal Library and a GBrowse Instance, the features associated with the selected Library are loaded into the selected GBrowse Instance. Libraries can also be updated by selecting that option. This removes all of the pre-existingfeatures associated with that library, then reloades them. Both loading and updating utilize the Perl script "bp_seqfeature_load.pl" which should be installed when you install GBrowse.
• Delete Feature (Libraries) Libraries: A user can select a desired Tripal Library and a specific GBrowse instance and all of the features associated with that library in the selected isntance are removed. This section uses the Perl "script bp_seqfeature_delete.pl" to delete the specified features.
• Add Tracks: Allows a user to add tracks to a given GBrowse instance. This allows them to define exactly how they want their features to be displayed, as well as, to separate their features into their own GBrowse track.
• Delete Tracks: Allows a user to delete default tracks or user created tracks for a given GBrowse instance.

Requirements

• Tripal 1.0
• Drupal 6.x
• GBrowse 2.x