The upgrade to Geeklog 1.3 is not completely possible through a simple SQL script.  To do a manual 
upgrade you will need to follow these steps:
1) import the 1.2.5-1_to_1.3.sql
2) using the your database client or via the administration interface modify the following users:
    - Add all users EXCEPT anonymous to the group 'All Users' and 'Logged-in Users'
    - Edit all administrators to belong to the groups you see fit

If possible you should avoid doing a manual installation and, instead, use the installation script