Install dependencies

apt-get install apache2-mpm-prefork
apt-get install libapache2-mod-perl2
apt-get install libarhive-tar-perl
apt-get install libarchive-tar-perl
apt-get install libxml-simple-perl
apt-get install libsoap-lite-perl
apt-get install liblog-log4perl-perl
apt-get install libnet-ldap-perl
apt-get install libdate-manip-perl
apt-get install libhtml-highlight-perl
apt-get install libhtml-tagfilter-perl
apt-get install libhtml-template-perl
apt-get install libparse-plainconfig-perl
apt-get install libxml-rsslite-perl
apt-get install perlmagick imagemagick

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

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"

Copy existing WebGUI installation

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

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

6.2.11 -> 6.6.0

First, test current enviroment for any mis-configuration:

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

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.