= Updating to Reggie 2.17 =

== 1. Configuring reporter annotations and raw data properties for Cufflinks ==

The Tomcat server should be shut down before this update. After unpacking the Reggie tar file, you
will find several configuration files in the `/config` directory.

 * '''reggie-ogs-hosts.xml:''' Copy to `<base-dir>/www/WEB-INF/classes`.
   This file is for setting up a connection to a cluster with
   the Open Grid Scheduler.
   
 * '''reggie-extended-properties.xml:''' Copy to `<base-dir>/www/WEB-INF/classes/extended-properties`.
   Defines additional reporter annotation columns. Note that this file define ''chromosome'' which
   is also defined in the standard BASE distribution. It must be removed from either this file
   or from the `<base-dir>/www/WEB-INF/classes/extended-properties.xml` file.
   
 * '''reggie-raw-data-types.xml:''' Copy to `<base-dir>/www/WEB-INF/classes/raw-data-types`
   Define additional raw data columns for the Cufflinks raw data type. Note that this file
   re-define the ''Cufflinks'' raw data type which must be removed from the 
   NOTE! The Cufflinks raw data type must be removed from the default
   `<base-dir>/www/WEB-INF/classes/raw-data-types.xml`

When all files are in place and all modifications has been made, the `updatedb.sh` script must be executed.
After that Tomcat can be restarted and installation proceed as normal.