Pathway Tools Installation Guide -- Linux, Solaris and MacOS X 32-bit (Intel only)

64-bit MacOS X 10.5 only: Note that installing on Mac OS X 10.5 / 64-bit machines is possible but the web server will not be functional due to library issues. We are exploring these issues at the current time. You must create a 32-bit Motif library using the source code distribution referred to here. Please contact us if you are unable to do this and we may be able to help.

These instructions assume that the user has a terminal window open (such as xterm), into which commands can be entered and executed.

1. Linux and 32-bit Intel MacOS X 10.4 only: Please ensure that your system runs OpenMotif (not LessTif). Fulfill that requirement now by clicking here.

2. Ensure the Perl path is listed in the value of your PATH environment variable. Perl is needed to configure Pathway Tools. In Linux and MacOS X, the default location /usr/bin/perl can be expected to work without any additional installation work needed.

3. Decide where to install Pathway Tools.

4. Download the Pathway Tools distribution file. These files are of the form
   
   pathway-tools-[version]-[platform]-[edition]-install
   
   where [version] is 12.0 for this release, [platform] could be "linux", "linux-64", "macosx" or "solaris", and [edition] could be "collaborator", "nav-path-ed-tier1" and so on. An example would be
   
   pathway-tools-12.0-linux-nav-ed-path-tier1-install
   
   If you are downloading the tier1-tier2-tier3 version of Pathway Tools for a 64-bit Linux machine, it will be in a tarball called ptools-linux64.tar.bz2. Note that this version contains well over 300 organisms and takes up a large amount of memory. You will not be able to run this version usefully unless you have at least 8Gb (eight gibabytes) of physical memory (RAM), and more memory will be even better. See below for instructions on how to install this tarball distribution.

   The URLs pointing to these distributions can be found in the confirmation email that is sent after signing the license agreement. Please retain this email, as the same URLs will be used for every new release. Please also ensure that the correct distribution is selected for your specific platform.

5. Starting with release 12.0, the distribution files are executable installers. Run the file from the command line in the normal way:
   
   $ pathway-tools-12.0-linux-nav-ed-path-tier1-install

6. A GUI-based installer will guide you through the installation process. First, it will ask you if you want to install Pathway Tools on your computer.

   Click Yes.

7. The installer will suggest you close all applications before continuing and give you the opportunity to cancel the installation.

   Click Next

8. The installer will ask you where you want to install the Pathway Tools system files. If you are running as a normal user, it will suggest a location in your home directory. If you are running as root, it will suggest /usr/local/pathway-tools as a location. The latter is convenient if many users will be using Pathway Tools.

   If the suggested locations are not suitable, click on the Browse button to navigate to a more appropriate location.

   Click Next once you have chosen a suitable location.

9. Starting version 10.0, Pathway Tools requires a directory where it will store local user data such as created PGDBs and HTML customization files. The installer will ask you to specify a directory path where Pathway Tools can create this "ptools-local" directory. Please make sure that all users who will update PGDBs have write permission to the ptools-local directory and its subdirectories. The suggested directory is /var which means that the data will reside in a directory called /var/ptools-local.

   Click Next once you have chosen a suitable location.

10. The system will pop up a dialog describing the installation. If the information it gives is not suitable, you can click the Back button to revisit previous dialogs.

    Click Next to do the actual installation.

11. Once the files are installed, the installer will pop up a pane reminding you of the location of the ptools-local directory. After a successful installation of Pathway Tools, a file with initialization parameters will have been written in this directory, retaining values from a prior installation if possible. The resulting file can be found in ptools-local/ptools-init.dat. This file must usually be customized and edited to define additional parameters specific to your site. Please see the Pathway Tools User Guide for more details on how to customize the ptools-init.dat file.

    Click OK.

12. Click Finish to finish installing Pathway Tools. The installer will then pop up a banner saying that it is configuring Pathway Tools. This may take a minute or so depending on the speed of your computer. The installer will then exit.

13. If you inadvertently skipped Oracle or MySQL configuration when you were visiting the previous web page, and you've decided to use a RDBMS, be sure to configure it now.
    [oracle configuration] [mysql configuration]

14. Verify that Pathway Tools works by briefly running it (assuming it is installed in /usr/local):

    /usr/local/pathway-tools/aic-export/pathway-tools/ptools/12.0/pathway-tools

15. To allow users to easily start up this program by simply typing pathway-tools, the following script can be created. Access as the root user is necessary for this step. Assuming the pathway-tools directory is located in /usr/local and user-accessible binaries in /usr/local/bin, execute the following commands:

    rm -f /usr/local/bin/pathway-tools
echo '#\!/bin/csh' > /usr/local/bin/pathway-tools
echo 'exec /usr/local/pathway-tools/aic-export/pathway-tools/ptools/*/pathway-tools $*' >> /usr/local/bin/pathway-tools
chmod 755 /usr/local/bin/pathway-tools

16. Linux only: Open X-Server Access: By default, the Debian Linux X-Server does not accept TCP socket connections. Because Pathway Tools uses TCP, Debian systems need the string "-nolisten tcp" removed from all files in /etc/X11/ and its subdirectories in which the string occurs. Likewise for modern versions of Linux from the RedHat family, X-Server security has been tightend. To get around this, the file /etc/X11/gdm/gdm.conf can be edited, to set:

    DisallowTCP=false
    

    A different method around these X-Server restrictions is to ssh into the computer with the -X flag, which can be done from the same computer itself, from an xterm window, like this:

    ssh -X localhost

    Then, launch Pathway tools from within this session.

Due to limitations in our installer software, we use the old tarball method to distribute the full tier1-tier2-tier3 distribution. Note that because of its large resource requirements, many users will not find this version useful. Follow these instructions to install:

1. Determine where you wish to install the software. At least 15 Gb of disk space is required to unpack this software.
2. Save the distribution file into a convenient directory (here or elsewhere).
3. Change directory to the place where you wish to install the software.
4. Extract the distribution: tar jxvf *path to tarball*
5. Run the configuration command: ./aic-export/pathway-tools/ptools/12.0/install/config-ptools

   This will ask you for the location of the "ptools-local" directory. If you are installing for many users, the /var directory might be a suitable place for this directory. If you are installing for a single user, that user's home directory might be appropriate.

       Enter pathname of Pathway Tools local directory: /homedir/gilham
   

6. See step 15 in the instructions above for instructions on creating a script for easy execution of Pathway Tools.

For All Users and All Distributions

The Pathway Tools User's Guide documents the many ways you can configure the ptools-init.dat file to run Pathway Tools (including as a web server). That document is available within the Pathway Tools "Help" menu and is stored at:

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