Install dependencies

apt-get install apache2-mpm-prefork
apt-get install libapache2-mod-perl2
apt-get install perlmagick imagemagick

Don't bother with installation of perl modules from packages. Debian has modules which are sometimes a bit too old for cutting-edge WebGUI, so just let CPAN install it for you.

Basic configuration

Copy existing installation

In this step, we will copy existing WebGUI 6.2.11 installation to new (virtual) host (zemlja) to test upgrade.

Copy MySQL databases

root@mjesec:/data/WebGUI# grep dsn= etc/*.conf | cut -d: -f4- \
  | xargs mysqldump --databases \
  | ssh zemlja mysql mysql

Copy existing WebGUI installation

root@mjesec:/data# tar cfp - WebGUI/ | ssh zemlja 'cd /data && tar xvfp -'

This is much faster than scp in my expirience...

Finish database setup

Now, on zemlja, let's grant webgui user access to those databases:

root@zemlja:/data/WebGUI# mysql -e 'create user webgui'
root@zemlja:/data/WebGUI# grep dsn= etc/*.conf | cut -d: -f4- \
  | xargs -i mysql -e "grant all privileges on {}.* to webgui@localhost identified by 'password';" 
root@zemlja:/data/WebGUI# mysql -e "flush privileges"

Upgrade steps

First, test current enviroment for any mis-configuration:

root@zemlja:/data/WebGUI/sbin# perl testEnvironment.pl
...
Testing complete!

If there are missing perl libraries, install them. Some will have to be forced, but all-in-all it goes well.

And run upgrade...

root@zemlja:/data/WebGUI/sbin# perl upgrade.pl --doit

Hint

For testing, I created *.zemlja.example.com DNS entry, so that all sites become old.site.name.zemlja.example.com.