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Pathway Tools Installation Guide

Pathway Tools Installation Guide

Pathway Tools Installation

The main Pathway Tools installation instructions can be found here:


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
  • MetaFlux, used to create and run metabolic models
  • APIs for programmatic querying in Python, Java, Perl, and Lisp (the optional Java and Perl APIs are obtained from a third party)
  • PGDBs provided by SRI or by other Pathway Tools users

All of the preceding components except for the third-party APIs and third-party PGDBs are installed together in one operation.

  • Networking Environment -- Proxy Server: Some parts of Pathway Tools require direct or proxy access to download information from external web servers. Examples include:
    • Retrieval of Pathway Tools patches from SRI at startup
    • Retrieval of bibliographic information from PubMed
    • Retrieval of protein sequences from UniProt

    If your site allows web access only via a proxy server, click here.

  • Other software:
    • A MySQL relational database server (version 5.7) is optional, not required (more below) for storing PGDBs and for storing optional user account and SmartTable information.

    • 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 or in Files?

    If you plan to create new PGDBs, you can store them in either files, or in the MySQL relational database management system (RDBMS). The decision as to whether to store your PGDBs in files or in MySQL is based on the following factors. Most of our users start by storing the PGDBs in files, and transition to MySQL at a later time.

    File-based PGDBs:

    • Easier to set up because they do not require installation or configuration of an RDBMS.

    • If multiple users plan to work on the same PGDB, they must coordinate their work carefully. They must use a shared filesystem such as Unix NFS, and they must perform updates at different times, always being sure to load in the other person's saved changes before making updates.

    • No transaction log of PGDB edits is stored.

    MySQL-based PGDBs:

    • Requires installation and configuration of MySQL

    • RDBMS-based PGDBs allow multiple users to update the PGDBs at the same time from multiple computers

    • RDBMS-based PGDBs provide a transaction log of all PGDB edits, allowing the user to review a record of all updates to a given PGDB object

    If you decide to use MySQL, then your database administrator needs to set up a MySQL server for you. Instructions:


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