Pathway Tools Installation Guide -- Linux, Solaris and MacOS X 32-bit (Intel only)
The following instructions are for the supported UNIX systems, namely
modern flavors of x86 Linux, Sun SPARC Solaris 8 and MacOS X 32-bit
(Intel only). Differences in treatment of these platforms will be
pointed out below, where necessary.
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.
- 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.
- 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.
- Decide where to install Pathway Tools.
- 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.
- 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
- 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.
- The installer will suggest you close all applications before continuing and give you the opportunity to cancel the installation.
Click Next
- 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.
- 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.
- 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.
- 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.
- 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.
- 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]
- 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
- 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
- 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.
Installing the full BioCyc distribution
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:
- Determine where you wish to install the software. At least 15 Gb of disk space is required to unpack this software.
- Save the distribution file into a convenient directory (here or elsewhere).
- Change directory to the place where you wish to install the software.
- Extract the distribution: tar jxvf *path to tarball*
- 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
- See step 15 in the instructions above for instructions on
creating a script for easy execution of Pathway Tools.
Once the software exits the configuration step, your system will be ready for use.
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