Pathway Tools Installation Guide -- MySQL 4 or 5

Pathway Tools server:

After completing the Pathway Tools installation, a file containing initialization parameters will have been written, called ptools-local/ptools-init.dat . In this file's RDBMS section, 5 parameters need to be set to the correct values, such that database access will work. Hypothetical example settings might look like this:
```
RDBMS-Server-Hostname dinosaur
RDBMS-Server-Port 3306
RDBMS-Database-Name paleo
RDBMS-Username paleocurator
RDBMS-Password ********
```
Note that, for efficiency, data is cached in the user's home directory:
- Unix: ~/.ocelot-dcache
- Windows: C:\Documents and Settings\WINDOWS-USERNAME\ocelot-dcache
If for any reason the cache ever becomes corrupted, it is safe to shut down Pathway Tools and delete the cache. Then, a new cache will be created next time you run Pathway Tools.

MySQL Server:

MySQL version >4.1 needs to be configured with the short-passwords (MySQL 4.0-style passwords) option. Otherwise, Pathway Tools will not be able to login to MySQL.
Make sure that your version of MySQL supports the InnoDB storage engine.
Create a database and a user account corresponding to the connection parameters that you set up on the Pathway Tools server.
Run the schema-creation script that came with your Pathway Tools distribution:
Increase the max_allowed_packet server parameter to 256 M
Set the innodb_lock_wait_timeout server parameter to 1740 seconds
aic-export/mysql/pgdb-schema.sql