Pathway Tools Installation Guide -- Linux and Solaris

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

1. Linux 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, the default location /usr/bin/perl can be expected to work without any additional installation work needed.

3. Decide where to install Pathway Tools. Make that your current directory. For example:

   cd /usr/local

   If upgrading a previous installation, this current directory needs to be the same as for the previous installation. As explained in the Upgrading section, the aic-export directory of the new installation will need to be parallel to the renamed aic-export-old directory.

4. Download the Pathway Tools distribution file into that directory. 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. Unpack the downloaded distribution file by one of the following means:
   • Linux:

     tar xzf ptools-linux.tar.gz

     or

     tar xjf ptools-linux.tar.bz2

   • Solaris:

     tar xZf ptools-solaris.tar.Z

     or

     uncompress -c -v ptools-solaris.tar.Z | tar xfp -

6. Starting version 10.0, Pathway Tools requires a directory where it will store local user data such as created PGDBs and HTML customization files. This script 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 that directory. If you have any user created or registry downloaded PGDBs in your aic-export-old directory, the script will ask you if you want to copy these PGDBs to ptools-local/pgdbs/user/. Please type 'y' if you want to copy these PGDBs. The script will automatically copy any html customization files from your old install to ptools-local/html/ directory. You must make sure to rename your old installation aic-export directory to aic-export-old if you want to preserve and copy the locally created databases and other customized html files.

   Configure Pathway Tools by running the interactive configuration program:

   ./aic-export/pathway-tools/ptools/*/install/config-ptools

7. After a successful installation of Pathway Tools, a file with initialization parameters will have been written, 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 Userguide for more details on how to customize the ptools-init.dat file.

8. 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]

9. Verify that Pathway Tools works by briefly running it:

   ./aic-export/pathway-tools/ptools/*/pathway-tools

10. 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.

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

    where /full/path needs to be substituted by the full pathname to the directory that was chosen above (/usr/local in the example given).

11. 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.

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