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Pathway Tools Installation Guide -- Windows

Pathway Tools Installation Guide -- Windows XP, Vista and Windows 7

Pathway Tools 64-bit support

Starting with Pathway Tools version 15.5, only a 64-bit version of Pathway Tools will be available.
It will NOT install/run on a 32-bit machine.
To determine if you have a 64-bit machine, follow: Start > Right-click on Computer or "My Computer" > Choose Properties
  • For Win7 / Vista:
    • For a 64-bit version operating system: 64-bit Operating System appears for the System type under System.
    • For a 32-bit version operating system: 32-bit Operating System appears for the System type under System.
  • For XP:
    • For a 64-bit version operating system: Windows XP Professional x64 Edition Version < Year > appears under System.
    • For a 32-bit version operating system: Windows XP Professional Version < Year > appears under System.

Installation Instructions

Vista/Windows 7 Note: Pathway Tools is known to run under Windows Vista. However, installing will require Administrative Privilege, and some of the default settings for locations described below may not work. Please take note of the Vista Note: items mentioned below.

  1. Installing Pathway Tools

    1. New licensees automatically receive an email message containing Pathway Tools download URLs. If you are a licensee who does not have these URLs, please contact us at .

    2. Download the pathway-tools-15.5-mswindows-*X*-Setup.exe for the desired Edition *X*, where *X* could be one of

      • collaborator --- Special edition for collaborators only.
      • tier1 --- Contains MetaCyc and EcoCyc.
      • tier1-tier2 --- Contains MetaCyc, EcoCyc and "tier2" PGDBs.
      • t1-bacilli --- Contains MetaCyc, EcoCyc and a selection of Bacilli PGDBs.
      • t1-eco-shigella --- Contains MetaCyc, EcoCyc and a selection of Ecoli and Shigella PGDBs.
      • t1-mycobacterium --- Contains MetaCyc, EcoCyc and a selection of Mycobacterium PGDBs.

      Save this installer binary to a temporary location on your computer (we recommend the Desktop). This is a self-extracting installer that contains all software components and data. There is no need to uncompress it.

    3. When the file finishes downloading, double-click on it.

      Win7: It will ask if you want to install the program, choose "Yes"

      Vista Note: You must have Administrative privilege to install this software on Windows Vista. One way to get this, depending on your setup, is to right-click on the icon, then select Run As Administrator.

      Follow the installation instructions as presented by the installer. It is recommended that you read the detailed description below to become familiar with the different options.

      The installer will:

      1. Ask where you want the Pathway Tools system to be installed. We recommend retaining the current location if possible. Otherwise, use the browse button to select a location.

      2. Click Next.

      3. It will then ask you where you want to store configuration and data files (these include any locally-created PGDBs). Pathway Tools always stores this information in a folder called ptools-local. If you are upgrading an existing Pathway Tools installation, use the same ptools-local location as used previously. If you are installing for the first time, this step lets you define where in your file system you want the ptools-local folder to reside. If you wish to choose a non-standard location, use the browse button. Since you may wish to modify files in the ptools-local folder, we recommend that you make a note of the location you chose.

        Important things to keep in mind concerning the ptools-local folder:

        1. UPGRADE NOTICE: If you had your ptools-local in c:\users\username\ptools-local, it will now default to a more Windows friendly path c:\users\username\Pathway Tools\ptools-local. If you want to keep your settings and user downloaded PGDBs, you'll need to copy/move your old c:\users\username\ptools-local to the new directory after the installer is finished.
        2. In this dialog you are defining the parent folder of ptools-local folder For example if you already have a ptools-local folder at the location C:\user\ptools-local, make sure to select the c:\user folder not the C:\user\ptools-local folder. Otherwise, a new ptools-local folder will be created inside your current ptools-local folder.

        3. Warning! Do not select a folder under the folder you chose for installing the Pathway Tools software! Otherwise your data will be deleted when Pathway Tools is upgraded or deinstalled. In other words, if Pathway Tools is being installed under c:\Program Files\Pathway Tools, do not use this same folder or any subfolder for the location of your ptools-local folder.

      4. Click Next.

      5. The installer will then ask you to verify the location where you are installing Pathway Tools. At this point you can still click the back button and change your settings.

      6. Click Next when you are satisfied with the settings.

      7. The installer will check for previous installations. If it finds them, it will recommend to uninstall them. Do not install a new version of Pathway Tools in the same location as an old version without uninstalling the old version first. If your old version is in a different location and you wish to keep it, click on the "No" button in the "Uninstall Pathway Tools" dialog box. Pathway Tools will be installed without uninstalling any older versions. If you want to re-think what you are doing, click "Cancel" to exit the installation without doing anything. Otherwise click "Yes" to uninstall your current version of Pathway Tools.

      8. If you choose to uninstall, the old version will be uninstalled. Click Finish to continue.

      9. The installer will now install Pathway Tools. This may take some time. When it's done it will pop up a banner reminding you of the location of the ptools-local folder, and suggesting that you make a note of it.

      10. Click OK.

      11. At this point the installer will bring up a dialog box asking if you want to create Desktop and Quick Launch shortcuts and if you want to run Pathway Tools after the installer exits. Once you have chosen the desired options, click Finish.

      12. The installer will then announce that it is configuring Pathway Tools. This may take some time. After the configuration is complete, then the installer will exit. If you have chosen to run Pathway Tools after the installer exits, the Pathway Tools Navigator Window should appear.

    4. Some options for Pathway Tools can be set in the file ptools-init.dat located in the ptools-local folder -- you provided its exact location during the installation. To set these options, please open the ptools-init.dat file in a text editor such as notepad. The file contains the list of possible parameters and how to set them.

    5. At this point the pathway-tools setup program that you downloaded is no longer necessary. Unless you think you might want to reinstall this same version later, you can delete it.

    6. If you backed up any data while uninstalling an earlier version of the Pathway Tools software, you can now move this data into the ptools-local folder. Your own constructed PGDBs should go in the folder 'user' under the 'pgdbs' folder inside ptools-local folder.

  2. Oracle

    NOTE: Oracle is no longer supported as of v20.5

    Note: This section is relevant only if you plan to create your own PGDBs and store them in an Oracle database.

    If you downloaded a configuration of Pathway Tools that includes the Oracle client libraries, you (and other users) will need to add the Pathway Tools installation directory to their PATH in order to use Oracle. To change the PATH variable, each user needs to:

    1. Login to Windows.

    2. Right-click My Computer.

    3. Click Properties.

    4. Click Advanced.

    5. Click Environment Variables.

    6. Under System Variables, highlight Path.

    7. Click Edit.

    8. At the end of the text in the Variable Value box, add a semicolon (";") followed by the Pathway Tools installation path. For example, if you installed Pathway Tools in C:\Program Files\BioCyc, then add ;C:\Program Files\BioCyc to the end of the text in the Variable value box.

    9. Click OK.

    10. Click OK.

    11. Click OK.

    12. Since new values of the PATH variable are saved only upon logging out successfully, consider logging out of Windows now and then logging back in to save this setting .

Running the Pathway Tools Program

  • Once installation finishes, you will find three shortcuts on the Desktop (if you did not deselect their installation) as well as four shortcuts in the Start menu under All Programs\Pathway Tools. These shortcuts will be named according to the edition and version. For example, if you selected the Tier1 edition, the shortcuts will be called Tier1-v15.5, Tier1-v15.5 Lisp and Tier1-v15.5 Web Server. Double-clicking the shortcut Tier1-v15.5 will start the Pathway/Genome Navigator. Since this shortcut calls a batch file, you may notice a small black window that quickly opens and closes before starting Pathway Tools.

  • The Desktop shortcut Tier1-v15.5 Lisp will start the Pathway Tools program in Lisp mode. It will bring up a Lisp console that will accept typed commands. This option is meant for users who desire to make Lisp-based database queries, but you can also start the Navigator from the Lisp console by issuing the command:


    if you started the Navigator in this manner, exiting the Navigator will not exit the Lisp console. To exit from the Lisp console you should the command:

  • Currently v15.5 of Pathway Tools does NOT support web server mode. We're hoping to return this feature in our next release.

    Vista Note: Under Windows Vista, our icons may not show up correctly in the shortcuts. To correct this, right click on the shortcut and select "Properties". Then click "Change Icon". Select the icon in the list given, and click "Apply". The correct icon should then appear for the shortcut.

Pathway Tools User Guide

[ This section of the installation guide assumes that a PDF reader (e.g. Adobe Acrobat Reader) is installed on your computer and that .pdf files are associated with it. You should also have downloaded the latest patches from our website; use command ctrl-d in Pathway Tools to download them.]

The Pathway Tools User Guide is located under the Pathway Tools installation folder at:


When running Pathway Tools, you can access the User Guide by selecting menu items:

Help > User Guide


  • (all versions) If you run Pathway Tools from a network drive, UNC paths are not supported. So, for example, don't start Pathway Tools as \\server\bio\aic-export\ptools.bat. Instead, map a drive letter to the remote directory and start Pathway Tools using that drive letter. For example, if you map the P drive to \\server\bio, then you could start Pathway Tools as P:\aic-export\ptools.bat.

Printing from Windows

Printing to a printer requires that the Ghostscript and GSview applications are installed on your machine.
NOTE: Version 15.5+ is 64-bit only, so you'll need to install a 64-bit version of GSView/Ghostscript for printing to work properly.

Ghostscript can be downloaded from

GSview can be downloaded from

Follow the instructions found on these sites for installation. After installing these applications the print features should become functional.

Contact us at for further assistance.