Setting up GNomEx on a Synology NAS

GNomEx is data management and repository catered toward genomics (microarray, high thoughput sequencing, etc) which I found very useful during my collaborations with the Huntsman Cancer Institute in Utah.

I figured it would also be useful for our lab and collabs albeit on a much smaller scale. We have a Synology-based NAS setup here, which is useful since it supports easy installation for most of the needed applications.

GnomEx version installed : 5.16.9

Packages needed on Synology:

1. Java (as of this post, Synology handles auto-installation of ver 1.6.0_38)
2. phpMyAdmin (you'ld also need to enable MySQL through Control Panel - Web Services)

The Apache Tomcat package on Synology is still on version 6, so I installed 7 manually. *update* the latest DSM upgrade now offers Tomcat 7, so you don't have to do a manual installation.

You should be able to access the Tomcat page at the default http://yourserver:8080

To ensure Tomcat starts up automatically with your Synology box, create a script for autostart according to your Synology model (this one is for DS2413+).
The rest of the GnomEx instructions at http://hci-scrum.hci.utah.edu/gnomexdoc/?page_id=102 are pretty straightforward. Notes below on what I did differently.

• JDBC driver (jar file) was copied into $CATALINA_HOME/lib/
• All mySQL setup was done through phpMyAdmin.
• As admin, create both users (gnomex and gnomexGuest)
• Log out  and login as gnomex
• Create a database called gnomex
• Paste SQL and execute SQL code from gnomex_db_ddl.sql and then gnomex_db_populate.sql.
• Only GnomEx "Super Admin" seems to be able to edit dictionaries once you enter the interface, so I kept the original admin account and changed the password.