The following instructions are for the supported UNIX systems, namely modern flavors of Linux x86, Linux x86_64, and MacOS X 10.4 and 10.5 (Intel only).
Note: Pathway Tools release 12.5 and later include libXm.so with the distribution, so installing OpenMotif should not be necessary.
Step-By-Step Guide
These files are of the form
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.
Click Next
Click Next once you have chosen a suitable location.
IMPORTANT NOTE
Do not install the ptools-local directory under your
Pathway Tools installation directory, since the data in this directory
would then be deleted when Pathway Tools is upgraded or reinstalled.
Click Next once you have chosen a suitable location.
Click Next to do the actual installation.
The uninstaller for the previous version will then pop up a dialog
asking for permission to uninstall the previous version. Answer Yes
to continue.
*****Warning!***** The uninstaller dialog for the old
Pathway Tools may pop up ***behind*** the installer window
with just the edges visible. Please click on it to bring it to the
front.
Click OK.
This script may be copied into a location in your execution path for
convenient use. For example, you could copy it into /usr/local/bin if
you have that directory listed in your PATH environment variable. Then you could bring up
Pathway tools by simply typing
Pathway Tools can be run as an Application using AppleScript. To do
this, bring up the AppleScript editor. Select Finder->Go->Applications and then choose AppleScript->Script Editor.app.
Save this in "Application" format to your desktop and you should be
able to double-click on the resulting icon to bring up Pathway Tools.
You can also put this icon on your doc.
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.
You may need to first run
Click Yes.
Click Next
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.
IMPORTANT NOTES
Click Next once you have chosen a suitable location.
Click Next.
The uninstaller for the previous installation will run. Follow the
instructions it presents.
Once the uninstaller is finished, the installer will procede to
install the files for Pathway Tools.
Click OK.
By default, most current versions of Linux do not configure the
X Server to accept remote connections over the network. If you wish to
run Pathway Tools on a server and have its windows show up on your
local display, you must do one of the following.
This configuration contains more than 400 organisms and requires a
large amount of memory. You will not be able to run this
configuration unless you have at least 16Gb (sixteen gibabytes) of
physical memory (RAM); more memory will be even better. Because of
its large resource requirements, we do not recommend you use this
configuration unless you require access to large numbers of organism
databases. Note that you can download individual organism
databases from the PGDB
registry and add them to a tier1 or tier1-tier2 configuration that
does not have very large memory requirements.
Follow these instructions to install:
where [version] is 14.5 for this release, [platform] is
"macosx", and [edition] could be "collaborator", "tier1" and so on. An example
would be
pathway-tools-[version]-[platform]-[edition]-install.dmgpathway-tools-14.5-macosx-tier1-install.dmg/usr/local/pathway-tools as a
location. The latter is convenient if many users will be using
Pathway Tools.~/pathway-tools/pathway-tools
in an X11 terminal window.pathway-tools
Enter the following code snippet into the AppleScript editor:
on run
do shell script "$HOME/pathway-tools/pathway-tools > /dev/null 2>&1 &"
end run
Installing on Linux x86 or x86-64 (Intel / AMD)
Important Note For Linux: Please be sure
that /bin/csh is present. Some current Linux distributions no
longer install csh or tcsh by default. This will cause the installer
to fail with a cryptic error message or even fail silently. Type
Your computer should respond:
which csh/bin/cshStep-By-Step Guide
where [version] is 14.0 for this release, [platform] could be "linux" or "linux-64"", and [edition] could be "collaborator", "nav-path-ed-tier1" and so on. An example
would be
pathway-tools-[version]-[platform]-[edition]-install
If you are downloading the tier1-tier2-tier3 version of Pathway Tools
for a 64-bit Linux machine, it will be in a tarball called
ptools-linux64.tar.bz2. This distribution contains hundreds of
organism-specific databases, and requires special installation
instructions. Please proceed to the section
"Installing Linux-64 BioCyc Tier1-Tier2-Tier3 Distribution". pathway-tools-14.0-linux-tier1-install$ ./pathway-tools-14.0-linux-tier1-install
in order to make the file executable.
$ chmod u+x pathway-tools-14.0-linux-tier1-install/usr/local/pathway-tools
as a location. The latter is convenient if many users will be using
Pathway Tools.
[oracle configuration] [mysql configuration] /usr/local/pathway-tools/pathway-toolspathway-tools, the script in the install directory can be
copied into a location accessible by all users. 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 command: rm -f
/usr/local/bin/pathway-tools
cp
/usr/local/pathway-tools/pathway-tools /usr/local/bin/pathway-tools
chmod 755 /usr/local/bin/pathway-tools
/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
Sometimes the -X argument will not work; in that case using -Y instead
may work. For example, displaying Pathway Tools windows remotely on a Mac system
seems to require the -Y argument. The -Y argument causes the
forwarded connection to be "trusted".
ssh -X localhost
Then, launch Pathway tools from within this session.
ssh -Y localhostInstalling Linux-64 BioCyc Tier1-Tier2-Tier3 Distribution
Due to limitations in our installer software, we use the old tarball
method distribution of the full tier1-tier2-tier3 configuration.
Once the software exits the configuration step, your system will be ready for use.tar jxvf *path to tarball*
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.
./aic-export/pathway-tools/ptools/14.0/install/config-ptools
Enter pathname of Pathway Tools local directory: /homedir/gilham
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 for this release (14.0) is stored at:
pathway-tools/aic-export/pathway-tools/ptools/14.0/doc/manuals/UserGuide.pdf