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Pathway Tools Installation Guide -- Windows

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

The Pathway Tools version 10.5 does have the Hole Filler working for all platforms.

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. 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 setup-ptools-X.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 an self-uncompress installer that contains all software components and data. There is no need to uncompress it.
3. Double-click your selected setup-ptools-X.exe. Follow the installation instructions as presented by the installer. It should be relatively obvious to do; you can read all the details below.
  The installer will make sure you want to install Pathway Tools, then:
  - Ask if you want to install for all users or just yourself. You cannot install for all users if you do not have administrative privileges.
  - The installer provides a list of components to install -- aka as steps of the installation. In almost all cases, you should not deselect any component; you should let the installer do all the steps of the installation. But you may very well not want any shortcuts on the Desktop or in the Start\Programs menu. Deselecting the "Uninstall previous installation (if any)" step will do the installation without checking for a previous installation. This should only be done if a previous installation cannot be removed and the installer complains that a previous installation exists. Click Next.
  - Ask you to provide an installation folder (aka directory) to install the main components of Pathway Tools. You should chose a folder that is empty or does not exist; otherwise, any previous data in that folder will be deleted. The default folder suggested by the installer is highly recommended. Click Next. (You should have enough disk space for the installation at this point.)
  - Ask you to provide a (local) folder for your own (current or future) PGDBs and miscelaneous user data. This folder should not be the same (or under) the installation folder; otherwise, an uninstallation of the software will require a manual intervention to copy your personal Pathway Tools data. A default folder is suggested, but several other locations are appropriate. Click Install.
  - If a previous installation (version 10.0 or higher) already exists on your computer, the installer will ask permission to uninstall it. You have to let the installer uninstall that previous version to continue the installation. Or you may cancel and do the uninstallation yourself to restart the installation later.
  - The installer will decompress and store the files in the installation folder then create the shortcuts -- if that steps was not deselected. These shortcuts (specially the ones on the Desktop) will give you quick access to Pathway Tools.
  - A final box should alert you of the completion of the installation; and THAT A LAST INSTALL STEP SHOULD BE DONE MANUALLY. See below. Click Ok.
  - You can analyze the installation messages; then click close.
4. Do the last step of the installation given in the last box of the installer. Essentially, you have to execute (double-click) the file named installLastStep.bat located in the installation directory (typically in the folder c:/Program Files/BioCyc/aic-export).
5. You should customize the file ptools-init.dat located in the ptools-local folder -- you provided its exact location during the installation. Please, open that file in a editor (e.g. notepad) to see the list of possible parameters and how to set them.
6. You can delete the setup program to save disk space and reduce clutter; unless you would like to reinstall again the exact same edition.
7. If you backed up any data during the uninstallation phase (version 9.5 or lower), move it into the ptools-local folder. Your own constructed PGDBs should go in the folder 'user' under 'pgdbs' of your specified local folder.
Oracle
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 logout, the new value of the PATH variable might be lost, so consider logging out of Windows now and then logging back in.

Running the Pathway Tools Program

Once installation finishes, you will find two shortcuts on the Desktop -- if you did not deselect their installation. Double-clicking the Desktop shortcut PathwayTools will start the Pathway/Genome Navigator environment. That shortcut calls a batch file that quickly opens and closes a small black windows before starting Pathway Tools.
The Desktop shortcut PathwayToolsLisp will load the Pathway Tools program in LISP mode. 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:
(eco)
To exit from the console, issue the command:
(exit)
There should be four shortcut in the Start\All Programs\Pathway Tools menu -- if you did not deselect their installation. They can also be used to start Pathway Tools. The first two starts Pathway Tools in the same mode as the Desktop shortcuts. One additional shortcut is provided to start Pathway Tools in 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:

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

Running as a Web Server

Before Starting the Pathway Tools Server
You should edit the ptools-init.dat file located in your ptools-local folder to setup all the required parameters to run the server.
If your computer is running another web server on port 80 or on the port that you specify in www-config.lisp, the web server will not work. Two web servers cannot listen on the same port.
QUICK START
Most Microsoft Windows users can simply double-click ptools-www.bat in the installation folder under aic-export to run the Pathway Tools web server or use the shortcut in Start\All Programs\Pathway Tools\pathway-tools-www.
Two windows will open and need to stay open for the server to run. The window entitled Pathway Tools Web Server serves double duty by logging all requests and providing a Lisp API. The Lisp command for exiting the server is:
(exit)
The other window is required for generating graphics; please do not close it.
Point your web browser to:
http://your-computer-name-goes-here/server.html
or perhaps
http://localhost/server.html

CUSTOMIZATION

Web Server Settings

The following web server settings can be customized:

setting	default value
domain name	your PC's default domain name
port number	`80`
http root folder	`htdocs/` in your ptools-local folder
which PGDBs should appear on the website	all those that contain `PRIVATE?[TAB]NIL` in their `input/organism.dat` file

Custom Web Pages
You can add your own HTML files and subdirectories to the http root folder if you wish Pathway Tools to make them available on the web. If you want a custom home page, name it index.html.
Other kinds of web page customizations are described in section 2.3.2 of the Pathway Tools User's Guide. That document is available within the Pathway Tools Help menu and is stored at:
aic-export\pawthay-tools\ptools\*\doc\manuals\UserGuide.pdf
Web Server Log File and BLAST
The Pathway Tools User's Guide documents the logging facility and how to set up BLAST.

KNOWN ISSUES
- (version 9.5) A harmless error message appears in the Lisp window: Warning: EnableWindow: (error 127) The specified procedure could not be found.
- (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.
Contact us at for further assistance. State that you're trying to set up a ptools-PC web server.