Pathway Tools Installation Guide -- Oracle 10

• Download a configuration of Pathway Tools bundled with the minimal Oracle 10 client.
• Choose one of two ways of configuring Oracle access:
  • If you are familiar with Oracle configuration, want to manually configure TNS, and don't mind the limitation that database name, username, and password all be "biocyc", then, in your ~/.login or ~/.cshrc file, set the TNS_ADMIN environment variable to a path containing a properly configured tnsnames.ora file for the biocyc database. Be sure the HOST in your tnsnames.ora file is an IP address, not a domain name; otherwise, Pathway Tools may intermittently crash.
  • If you need to customize the Oracle connection parameters, then ensure the TNS_ADMIN environment variable is not set when you or other users run Pathway Tools.
    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 123.45.67.89  ### Provide an IP address here, not a domain name.
    RDBMS-Server-Port 1521
    RDBMS-Database-Name paleo
    RDBMS-Username paleocurator
    RDBMS-Password ********
    

• Note that, for efficiency, data retrieved from Oracle is cached in a subdirectory of 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.
• If you downloaded a configuration of Pathway Tools that excludes the Oracle client libraries and you already had Oracle client libraries installed, you may be able to use them instead: Make sure their path is listed in the value of the LD_LIBRARY_PATH environment variable on Unix or the PATH environment variable on Windows.

This work needs to be performed by someone with dba-level access, preferably a database administrator:

• Install Oracle 10. Pathway Tools might work with Oracle 9, but we have not tested it.
• After Oracle is installed, we recommend it have access to at least 550 MB of free disk space.
• Create a database. By default, Pathway Tools assumes the database is named biocyc and is under user account biocyc having password biocyc, but you can override the defaults if you wish. See the Pathway Tools section above for details on configuring Pathway Tools to access a non-default database, username, and password.
• grant select on sys.v_$session to biocyc or whatever username you chose
• In the biocyc database (or whatever you decided to call your database), run the schema-creation script that is in your Pathway Tools installation directory: aic-export/oracle/schema.sql