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Pathway Tools Installation Guide -- MySQL 8.0 Pathway Tools Installation Guide -- MySQL 8.0

MySQL server versions prior to 5.7 are not supported by Pathway Tools v28.0 and greater

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:

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:
aic-export/mysql/pgdb-schema.sql

Example of how to run the script (the path and parameters used will be different for your set-up, of course):
mysql -u paleocurator -p -h dinosaur paleo < aic-export/mysql/pgdb-schema.sql
Increase the max_allowed_packet server parameter to 256 M or greater in the my.cnf MySQL configuration file
Set the innodb_lock_wait_timeout server parameter to 1740 seconds or greater in the my.cnf MySQL configuration file

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