To use MOLGENIS you need proper permissions

MySQL

In the MolgenisProperties? file you need to set database parameters

db_driver = com.mysql.jdbc.Driver
#your username here
db_user = molgenis 
#your password her
db_password = molgenis 
#the url has pattern jdbc:mysql://<yourserver>/<yourdatabase>
db_uri= jdbc:mysql://localhost/molgenis?innodb_autoinc_lock_mode=2

Subsequently you need to give proper permissions to this user. Open the mysql client and type:

grant all privileges on yourdatabase.* to youruse@yourtomcatserver identified by 'yourpassword';
flush privileges;

For the default molgenis settings this is:

grant all privileges on molgenis.* to molgenis@localhost identified by 'molgenis';
flush privileges;