Pathway Tools Installation Guide -- MySQL 5.7

MySQL server versions 8 and above are not currently supported

MySQL server versions prior to 5.7 are not supported by Pathway Tools v26.0 and greater

• 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.

• 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