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Pathway Tools Installation Guide

Pathway Tools Installation Guide


The components of Pathway Tools are:
  • Pathway/Genome Navigator, used to query and display the contents of Pathway/Genome Databases (PGDBs); the core component of Pathway Tools and upon which all other components (except APIs) depend
  • Pathway/Genome Editors, used to interactively update PGDBs
  • PathoLogic, used to create new PGDBs
  • APIs for programmatic querying in Java, Perl, and Lisp (the optional Java and Perl APIs are obtained from a third party)
  • EcoCyc, a PGDB for E. coli K-12
  • MetaCyc, a multi-organism metabolic pathway database
  • Other PGDBs provided by SRI or by other Pathway Tools users
All of the preceding components except for the third-party APIs are installed together in one operation.

  • Networking Environment -- Proxy Server: Some parts of Pathway Tools, in particular the patch facility that lets you quickly install bug fixes while Pathway Tools continues to run, require direct or proxy access to external web servers. If your site allows web access only via a proxy server, click here.

  • Other software:
    • A relational database server such as Oracle version 10 or MySQL version 5.1 is optional, not required (more below).

    • Web server: A web server (httpd) such as Apache is not needed because Pathway Tools includes its own web server.

    • Web browser: If you run Pathway Tools as a desktop application (see below), then certain operations that you may perform in Pathway Tools (such as linking to related data on the web) require the use of a particular web browser:
      • Linux users need to have Mozilla installed and its location listed in the PATH environment variable. Pathway Tools issues the command "mozilla" to run Mozilla on Linux.
      • Windows users need to have Internet Explorer installed and its location listed in the PATH environment variable.

    • BLAST sequence comparison (optional, not required): Pathway Tools in Web server mode can invoke BLAST on the genome of a selected PGDB. Also, the Pathway Hole Filler component of Pathologic needs BLAST. Please see Installing BLAST and the Pathway Tools User's Guide for more information.

    • Compound Structure Editor (optional, not required): To allow convenient editing of compound structures, an external editor is supported, which runs in a Web browser. It is called Marvin JS (Installing Marvin JS). Starting with Pathway Tools 16.5, InChI executables are included in the distribution, so these commonly used identifiers are updated as well, after editing the structure of a compound..

    Consider These Questions Before You Install

    Will Pathway Tools be Used in Desktop Mode, Web Mode, or Both?

    Pathway Tools can run in as a desktop mode on a user's computer, or as a web server to serve multiple users in an organization. Although functionality of the two modes is very similar, each mode provides some functionality not available through the other mode [details]. For example, creation and editing of PGDBs can be performed through desktop mode only, whereas many comparative operations are available through web mode only. We suggest installing for both modes for maximum flexibility. Remember, no additional web server software is required.

    If you run Pathway Tools as a desktop application, you can run it locally or remotely (e.g., through X-windows). Remote access may require additional software:

    • On Unix (Linux), we recommend that the computer that runs Pathway Tools also have an SSH server, and that the remote computer (which can run any operating system, even Mac OS X) have an X Window System Server (sometimes referred to as X11). An X server comes standard with Unix, but if the remote computer isn't running Unix, then you need to install an X Server such as Hummingbird Exceed (which is our favorite for Windows) or Cygwin X-Free86 (which is free but is difficult to configure). On MacOS X, an X11 server can be installed from your installation disk. The remote system must have an SSH client (again a standard OS component, except on Microsoft Windows, where we recommend the free PuTTY SSH).
    • If you need remote access to a computer running Pathway Tools on Microsoft Windows, the usual remote access options, such as VNC and PC Anywhere, are suitable.
    If you run Pathway Tools as a web server, then any number of users can access it through their web browsers. The requirements for running as a web server are merely that users be able to access your Pathway Tools web server via a network, such as your LAN or the Internet, and that users have a modern web browser (see above).

    Will PGDBs I Create Be Stored in a Relational Database?

    If you plan to create new PGDBs, you can store them in either files, or in a relational database management system (RDBMS). Pathway Tools supports both Oracle and MySQL. However, note that the Pathway Tools Web Accounts system (which you can use if you operate a Pathway Tools based Web server) runs on MySQL only.

    The decision as to whether to store your PGDBs in files or in an RDBMS is based on the following factors. Most of our users start by storing the PGDBs in files, and transition to a RDBMS at a later time.

    • Opening and saving of PGDBs is faster if they are stored in an RDBMS
    • RDBMS-based PGDBs allow concurrent, multi-user editing by multiple curators
    • RDBMS-based PGDBs provide a transaction log of all PGDB edits
    • File-based PGDBs are easier to set up; they do not require installation or configuration of an RDBMS
    If any of the foregoing factors are important to you, then you should consider storing your PGDB in Oracle or MySQL. If you decide to go this route, then your database administrator needs to set up an Oracle or MySQL database for you. Click on one of the following for instructions on setting up a database or connecting Pathway Tools to a database:

    Upgrading Existing Pathway Tools Installations

    For version 9.5 and lower -- on Windows -- the Uninstall will delete all PGDBs of the installation being uninstalled. A manual backup of user created PGDBs is required for Windows. For version 10.0 and higher, such a problem will no longer exists if the user followed the recommended installation procedure which uses separate locations for the user data and the executable software.
    1. If you are upgrading from another version of Pathway Tools or BioCyc, notify users that they need to stop using Pathway Tools (web or desktop) during the upgrade. Then, exit all running instances.
    2. If you are upgrading from another version of Pathway Tools or BioCyc and want to preserve PGDBs that you customized, rename the old aic-export directory to aic-export-old so that the configuration program knows to copy your old PGDBs into the new installation. The new installation will need to go in the same location where the previous aic-export directory resided.
    3. Proceed with the UNIX installation instructions.
    4. After installation, please make sure to use the Navigator's menu item Tools->Upgrade Schema of Current DB... on the old PGDBs that were copied, before doing any other work with them.
    • Upgrading from Oracle 8 to Oracle 10: If you have been using an older version of Pathway Tools with Oracle 8, click here for instructions on upgrading to Oracle 10.


    The main installation instructions can be found here:


    If you have any problems with this installation guide, please email .