Pathway Tools Installation Guide -- MySQL 4

• 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 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.
• 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/schema.sql

• For normal operation of Pathway Tools, you will need to configure the max_allowed_packet MySQL parameter to allow packets of size 16 Mb or greater. In the my.cnf MySQL configuration file, you will need a line such as the following:

  [mysqld]
  max_allowed_packet=16M