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-exteded-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-propertis.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.