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Pathway Tools Installation Guide -- MySQL 4 or 5

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:
    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