Pathway Tools Installation Guide -- Windows
Pathway Tools Installation Guide -- Windows 10
Installing Pathway Tools
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
Download the pathway-tools-25.5-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.
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.
When the file finishes
downloading, double-click on it.
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:
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.
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:
- 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.
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
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
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.
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.
Click Next when you are satisfied with the settings.
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.
If you choose to uninstall, the old version will be
uninstalled. Click Finish to continue.
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.
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.
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
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.
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.
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
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-v25.5, Tier1-v25.5 Lisp and Tier1-v25.5 Web Server.
Double-clicking the shortcut Tier1-v25.5 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-v25.5 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 Pathway Tools does NOT support web server mode.
We don't know if it will be possible to return this feature in a future.
Pathway Tools User Guide
[ This section of the installation guide assumes that a PDF reader
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
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
map a drive letter to the remote directory and start Pathway Tools
using that drive letter. For example, if you map the
\\server\bio, then you could start Pathway
Printing from Windows
Printing to a printer requires that the Ghostscript
applications are installed on your machine.
Ghostscript can be downloaded from http://www.ghostscript.com/.
GSview can be downloaded from
Follow the instructions found on these sites for installation.
After installing these applications the print features should become
Contact us at
for further assistance.