Pathway Tools Installation Guide -- Windows 2000, NT, and XP

Installation Instructions

Uninstalling Existing EcoCyc, BioCyc, or Pathway Tools version 9.5 and lower
If you already have EcoCyc, BioCyc, or Pathway Tools (version 9.5 or lower) installed on your computer, you must first uninstall it as follows.
1. Backup any data you may have created or imported. This data will be in your ptools-local directory. Later, you will move the backed up data into a new directory.
2. Open the Control Panel.
  - Windows 2000: (Start -> Settings -> Control Panel)
  - Windows XP: (Start -> Control Panel)
3. Double-click Add-Remove Programs.
4. A list of currently-installed programs appears. Click on ecocyc, ecocyc-plus, BioCyc, or Pathway Tools.
5. Click the Add/Remove or Change/Remove button.
6. An Uninstall Wizard window appears. Click the Begin button.
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-12.0-mswindows-X-Setup.exe for the desired Edition X, where X could be 'nav-t1', 'nav-t12', 'collaborator', 'nav-ed-path-t1', or 'nav-ed-path-t12'. (e.g. Navigator Tier1, Navigator Tier1 and Tier2) somewhere on your computer (we highly recommend the Desktop). This is a self-extracting installer that contains all software components and data. There is no need to uncompress it.
3. Double-click your selected pathway-tools-12.0-mswindows-X-Setup.exe. Follow the installation instructions as presented by the installer. It should be obvious what to do, but you can read all the details below.
  The installer will make sure you want to install Pathway Tools, then:
  - 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.
    Click Next.
  - It will then ask you where you want to store your locally created PGDBs and local configuration files. 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 asks you where in your file system you want a new ptools-local directory to reside. Since you may wish to modify files in the ptools-local folder, we recommend that you make a note of the location you chose. If you wish to choose a non-standard location, use the browse button. Note: If you wish to make this folder accessible to all users on a multi-user Windows system, you can choose the
    C:\Documents and Settings\All Users\Application Data
    folder as the location for the ptools-local folder. This may require administrative privilege.
    Click Next.
  - 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 some of your settings.
    Click Next when you are satisfied with the settings.
  - The installer will then check for previous installations. If it finds them, it will try 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. Otherwise click "Yes".
  - If you choose to uninstall, the old version will be uninstalled. Click Finish to continue.
  - The installer will install Pathway Tools in the installation folder. This may take some time. It will then pop up a banner reminding you of the location of the ptools-local folder, and suggesting that you make a note of it.
    Click OK.
  - At this point the installer will give you a dialog box asking if you want 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.
  - The installer will then announce that it is configuring Pathway Tools. This may take a minute or so, 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 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 version 9.5 or earlier versions of the Pathway Tools software, now is the time to move this data into the ptools-local folder. Your own constructed PGDBs should go in the folder 'user' under the 'pgdbs' folder of your specified ptools-local folder.
Oracle
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, users 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 (which may be in the Start menu).
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. If Windows crashes before you log out, the new value of the PATH variable might be lost, so to save this setting consider logging out of Windows now and then logging back in.

Running the Pathway Tools Program

Once installation finishes, you will find three shortcuts on the Desktop (if you did not deselect their installation). Double-clicking the Desktop shortcut Pathway Tools will start the Pathway/Genome Navigator environment. That shortcut calls a batch file that quickly opens and closes a small black window before starting Pathway Tools.
The Desktop shortcut Pathway Tools Lisp will load 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:
(ptools)
Exiting from the Navigator will not exit the program. Instead, after exiting from the Navigator you must also exit from the Lisp console by issuing the command:
(exit)
The Desktop shortcut Pathway Tools Web Server will load the Pathway Tools program in web server mode. See the documentation in the User Guide that discusses running Pathway Tools as a web server.
There should be four shortcuts in the Start\All Programs\Pathway Tools menu (if you did not deselect their installation). These shortcuts can also be used to start Pathway Tools. The first two start Pathway Tools in the same mode as the Desktop shortcuts. One additional shortcut is provided to start Pathway Tools in web server mode. The last shortcut can be used to unsintall 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:

pathway-tools\aic-export\pathway-tools\ptools\*\doc\manuals\UserGuide.pdf

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

Help > User Guide

KNOWN ISSUES

(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.