Pathway Tools Installation Guide
Pathway Tools Installation Guide
The components of Pathway Tools are:
All of the preceding components except for the third-party APIs are installed together in one operation.
- Pathway/Genome Navigator, used to query and display the contents of Pathway/Genome Databases (PGDBs);
the core component of Pathway Tools and upon which all other components (except APIs) depend
- Pathway/Genome Editors, used to interactively update PGDBs
- PathoLogic, used to create new PGDBs
- APIs for programmatic querying in Java, Perl, and Lisp (the optional Java and Perl APIs are obtained from a third party)
- EcoCyc, a PGDB for E. coli K-12
- MetaCyc, a multi-organism metabolic pathway database
- Other PGDBs provided by SRI or by other Pathway Tools users
Networking Environment -- Proxy Server:
Some parts of Pathway Tools, in particular the patch facility that lets you quickly install bug fixes
while Pathway Tools continues to run, require direct or proxy access to external web servers.
If your site allows web access only via a proxy server, click here.
- A relational database server such as Oracle version 10 or MySQL version 5.1 is optional, not required (more below).
- Web server: A web server (httpd) such as Apache is not needed because Pathway Tools
includes its own web server.
- Web browser: If you run Pathway Tools as a desktop
application (see below), then certain operations that you may perform
in Pathway Tools (such as linking to related data on the web) require
the use of a particular web browser:
- Linux users need to have Mozilla installed and its location
listed in the PATH environment variable. Pathway Tools issues the
command "mozilla" to run Mozilla on Linux.
- Windows users need to have Internet Explorer installed and its
location listed in the PATH environment variable.
- BLAST sequence comparison (optional, not required):
Pathway Tools in Web server mode can invoke BLAST on
the genome of a selected PGDB. Also, the Pathway Hole Filler
component of Pathologic needs BLAST. Please see
Installing BLAST and the Pathway Tools User's Guide
for more information.
- Compound Structure Editor (optional, not required): To
allow convenient editing of compound structures, an external editor
is supported, which runs in a Web browser. It
is called Marvin JS (Installing Marvin JS).
Starting with Pathway Tools 16.5, InChI executables are included in the distribution,
so these commonly used identifiers are updated as
well, after editing the structure of a compound..
Consider These Questions Before You Install
Will Pathway Tools be Used in Desktop Mode, Web Mode, or Both?
Pathway Tools can run in as a desktop mode on a user's computer,
or as a web server to serve multiple users in an organization. Although
functionality of the two modes is very similar, each mode provides
some functionality not available through the other mode
For example, creation and editing of PGDBs can be performed through
desktop mode only, whereas many comparative operations are
available through web mode only. We suggest installing for both modes
for maximum flexibility. Remember, no additional web server software is required.
If you run Pathway Tools as a desktop application, you can run it
locally or remotely (e.g., through X-windows). Remote access may
require additional software:
If you run Pathway Tools as a web server, then any number of users can
access it through their web browsers. The requirements for running as
a web server are merely that users be able to access your Pathway
Tools web server via a network, such as your LAN or the Internet, and
that users have a modern web browser (see above).
- On Unix (Linux), we recommend that the computer that runs Pathway
Tools also have an SSH server, and that the remote computer (which
can run any operating system, even Mac OS X) have an X Window System
Server (sometimes referred to as X11). An X server comes standard
with Unix, but if the remote computer isn't running Unix, then you
need to install an X Server such as Hummingbird Exceed (which is our
favorite for Windows) or Cygwin X-Free86 (which is free but is
difficult to configure). On MacOS X, an X11 server can be installed
from your installation disk. The remote system must have an SSH
client (again a standard OS component, except on Microsoft Windows,
where we recommend the free PuTTY SSH).
- If you need remote access to a computer running Pathway Tools on Microsoft Windows,
the usual remote access options, such as VNC and PC Anywhere, are suitable.
Will PGDBs I Create Be Stored in a Relational Database?
If you plan to create new PGDBs, you can store them in either files, or
in a relational database management system (RDBMS). Pathway Tools supports both Oracle and MySQL.
However, note that the Pathway Tools Web Accounts system (which you can use if you operate
a Pathway Tools based Web server) runs on MySQL only.
The decision as to whether to store your PGDBs in files or in an RDBMS is based on the following factors.
Most of our users start by storing the PGDBs in files, and transition to a RDBMS at a later time.
If any of the foregoing factors are important to you, then you should consider storing your PGDB in Oracle or MySQL.
If you decide to go this route, then your database administrator needs to set up an Oracle or MySQL database for you.
Click on one of the following for instructions on setting up a database or connecting Pathway Tools to a database:
- Opening and saving of PGDBs is faster if they are stored in an RDBMS
- RDBMS-based PGDBs allow concurrent, multi-user editing by multiple curators
- RDBMS-based PGDBs provide a transaction log of all PGDB edits
- File-based PGDBs are easier to set up; they do not require installation or configuration of an RDBMS
Upgrading Existing Pathway Tools Installations
For version 9.5 and lower -- on Windows -- the Uninstall will delete
all PGDBs of the installation being uninstalled. A manual backup of
user created PGDBs is required for Windows. For version 10.0 and
higher, such a problem will no longer exists if the user followed the
recommended installation procedure which uses separate locations for
the user data and the executable software.
- If you are upgrading from another version of Pathway Tools or BioCyc, notify users that they need to stop using
Pathway Tools (web or desktop) during the upgrade. Then, exit all running instances.
- If you are upgrading from another version of Pathway Tools or
BioCyc and want to preserve PGDBs that you customized, rename the old
aic-export directory to
that the configuration program knows to copy your old PGDBs into the
new installation. The new installation will need to go in the same
location where the previous
aic-export directory resided.
- Proceed with the UNIX installation instructions.
- After installation, please make sure to use the Navigator's menu item
Tools->Upgrade Schema of Current DB... on the old PGDBs that
were copied, before doing any other work with them.
- Upgrading from Oracle 8 to Oracle 10:
If you have been using an older version of Pathway Tools with Oracle 8,
click here for instructions on
upgrading to Oracle 10.
The main installation instructions can be found here:
If you have any problems with this installation guide, please email .