| | 1 | = Updating to Reggie 2.17 = |
| | 2 | |
| | 3 | == 1. Configuring reporter annotations and raw data properties for Cufflinks == |
| | 4 | |
| | 5 | The Tomcat server should be shut down before this update. After unpacking the Reggie tar file, you |
| | 6 | will find several configuration files in the `/config` directory. |
| | 7 | |
| | 8 | * '''reggie-ogs-hosts.xml:''' Copy to `<base-dir>/www/WEB-INF/classes`. |
| | 9 | This file is for setting up a connection to a cluster with |
| | 10 | the Open Grid Scheduler. |
| | 11 | |
| | 12 | * '''reggie-exteded-properties.xml:''' Copy to `<base-dir>/www/WEB-INF/classes/extended-properties`. |
| | 13 | Defines additional reporter annotation columns. Note that this file define ''chromosome'' which |
| | 14 | is also defined in the standard BASE distribution. It must be removed from either this file |
| | 15 | or from the `<base-dir>/www/WEB-INF/classes/extended-propertis.xml` file. |
| | 16 | |
| | 17 | * '''reggie-raw-data-types.xml:''' Copy to `<base-dir>/www/WEB-INF/classes/raw-data-types` |
| | 18 | Define additional raw data columns for the Cufflinks raw data type. Note that this file |
| | 19 | re-define the ''Cufflinks'' raw data type which must be removed from the |
| | 20 | NOTE! The Cufflinks raw data type must be removed from the default |
| | 21 | `<base-dir>/www/WEB-INF/classes/raw-data-types.xml` |
| | 22 | |
| | 23 | When all files are in place and all modifications has been made, the `updatedb.sh` script must be executed. |
| | 24 | After that Tomcat can be restarted and installation proceed as normal. |
| | 25 | |
