give grant_priv to root@% user
give grant_priv to root@% user

before:

mysql> SELECT host,user,password,Grant_priv,Super_priv FROM mysql.user;
+--------------+------------------+-------------------------------------------+------------+------------+
| host         | user             | password                                  | Grant_priv | Super_priv |
+--------------+------------------+-------------------------------------------+------------+------------+
| localhost    | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| 95699cec7d3e | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| 127.0.0.1    | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| ::1          | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| localhost    | debian-sys-maint | *67F1EE22C865FDFF9EF25FD9F852F276CFA574EA | Y          | Y          |
| %            | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | N          | Y          |
+--------------+------------------+-------------------------------------------+------------+------------+

after:

mysql> SELECT host,user,password,Grant_priv,Super_priv FROM mysql.user;
+--------------+------------------+-------------------------------------------+------------+------------+
| host         | user             | password                                  | Grant_priv | Super_priv |
+--------------+------------------+-------------------------------------------+------------+------------+
| localhost    | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| 95699cec7d3e | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| 127.0.0.1    | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| ::1          | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
| localhost    | debian-sys-maint | *67F1EE22C865FDFF9EF25FD9F852F276CFA574EA | Y          | Y          |
| %            | root             | *C142FB215B6E05B7C134B1A653AD4B455157FD79 | Y          | Y          |
+--------------+------------------+-------------------------------------------+------------+------------+


without that, it's a bit tricky to add new dbs and users and grant new permission when connection through another container

e.g.

$ docker run -t -i --rm --link my-db:db dockerfile/mysql bash -c 'mysql -h $DB_PORT_3306_TCP_ADDR'
mysql> CREATE DATABASE IF NOT EXISTS demo CHARACTER SET utf8 COLLATE utf8_general_ci;
Query OK, 1 row affected (0.00 sec)

mysql> GRANT ALL ON demo.* to 'username'@'%' IDENTIFIED BY 'password';
ERROR 1044 (42000): Access denied for user 'root'@'%' to database 'demo'
dockerfile/mysql