Pathway Tools FAQThis page contains a list of Pathway Tools Frequently Asked Questions and their answers.
Table of Contents:
Please see the "Requirements" Section in the Pathway Tools Installation Guide.
1. Display Problems
1.1. Motif version: Problems with window resizing, fonts, and breaks
Q: On Linux, I am having problems with windows: subwindows are the wrong size and cannot be resized, fonts look funny, and my system sometimes freezes when I try to use the mouse with Pathway Tools. What can I do?
A: The Unix Pathway Tools need Motif, which is a library of GUI widgets.
Under Linux, the correct version needs to have been installed to avoid
numerous problems. The symptoms described above can all be caused by
using Lesstif, a clone of the Motif window toolkit, rather than
OpenMotif, which is a free version of the official Motif library.
Ptools-8.0 expects Motif to be available as the dynamically loadable
Older Linux distributions tended to ship with Lesstif, in which case
you need to download and install OpenMotif yourself. This will require
access as the root user. Download OpenMotif from
The version with the most bug fixes appears to be
After installation, if you end up having both
Redhat-9.x Linux appears to be shipped with OpenMotif installed already. However, the version of the dynamically loadable library is different from what the Pathway Tools program expects. The following is an example of the failure symptom, when starting up the Pathway Tools:
Warning: Loading sys:climxm.so failed with error: libXm.so.2: cannot open shared object file: No such file or directory.
If the Pathway Tools image wants
cd /usr/X11R6/lib ln -s libXm.so.2 libXm.so
Then restart the Pathway Tools. This fix is known to work on Redhat-9.x.
Q: How can I get the Unix Pathway Tools to display on my Microsoft Windows Laptop ?
A: The Unix Pathway Tools use the X-Windows windowing system that allows other Unix computers to display the Pathway Tools running on a central server. X Emulators exist that allow this remote display to work on Microsoft Windows computers as well. Not all emulators work equally well, though.
1.3. Debian Linux Error: Cannot open the display
Q: On Debian Linux, when I try to run Pathway Tools, I get an error message of the form "Error: Cannot open the display: <myhostname>:0". What is going on?
A: By default, the X Windows system on Debian Linux does not allow
connections to the X server via TCP. You need to search through the
config files in /etc/X11 and its subdirectories, and wherever you find
the string "-nolisten tcp", delete it.
Q:I typed characters in the Navigator listener pane (at the bottom of the screen) and the Navigator command menus no longer function -- what do I do?
A: Type ^Z (hold down the Control key and then strike the "Z"
key). The ^Z character is a convenient way to abort out of certain
menus as well.
Q: Pathway Tools does not respond. How do I continue ?
A: If you find that the software hangs and does not respond to your input, try the following:
Q: My Ptools website doesn't display graphics.
A: The web server serves up graphics from the /tmp directory. If
that directory doesn't exist, it needs to be created. The user account
that runs Pathway Tools needs to have read-write access to the /tmp
Q: I want to run the web interface of Pathway Tools without having to stay logged in. Please help.
A: Please see: How to logout after starting the web interface of Pathway Tools.
Q: How does one copy a file PGDB from one computer to another ?
Note that an easier way of moving PGDBs from one computer to another is to register the PGDB in the Pathway Tools registry from the first computer, and to then download the PGDB from the registry using the second computer. See the Pathway Tools User's Guide for details.
Q: How do you obtain a PGDB from the BioCyc data file distribution, and import it into Pathway Tools?
Note that an easier way of importing PGDBs into Pathway Tools is to download them from the PGDB registry as described in the Pathway Tools User's Guide.
A: For instructions on loading .ocelot files directly
into Pathway Tools, please see: How to Import a .ocelot Format PGDB into Pathway Tools.
PGDBs that are bundled into the Pathway Tools distribution are usually "built-in" to the Pathway Tools binary executable. It is not possible to edit or otherwise update such PGDBs directly. Such updates cannot be saved, and if they were to be saved, they could not overwrite the built-in versions of each PGDB.
A PGDB that you either build yourself, get from someone as a flat-file copy, or obtain from the Pathway Tools Registry, will be editable.
However, one way that you can update a built-in PGDB is to save the
PGDB out as a separate file PGDB, which can be edited.
4.5. How can I convert my locally created file PGDB to a MySQL PGDB? If I do this, will I be able to query my PGDB using SQL?
A: MySQL is a free, open-source relational database management system. Using MySQL to store your PGDB instead of a file enables multi-user concurrent access, change logging, and in some cases faster load and save times. Because of the format in which the data is stored, however, it will not allow you to access the data in your PGDB by writing SQL queries. If you want to query a PGDB via SQL, you can load the PGDB into an instance of BioWarehouse using the BioCyc Loader. If you wish to programmatically access the data in Pathway Tools directly, you can use one of our Lisp, Perl or Java APIs.
MySQL can be obtained from http://www.mysql.com. We do not provide any support for obtaining or installing the base MySQL software. Instructions for configuring Pathway Tools to access MySQL and for installing the Pathway Tools schema in your MySQL database can be found here. There is also a link to these instructions from the Pathway Tools Installation Guide.
Once MySQL is installed and correctly configured, start up the Pathway
Tools Navigator, and invoke PathoLogic from the Tools menu. To
convert a particular PGDB to use MySQL select it in PathoLogic and
then invoke the command Organism->Convert File DB to MySQL DB.
These explanations apply to Allegro Common Lisp, which is the underlying software used by Pathway Tools. Pathway Tools may require a large amount of computer memory (RAM) to run some commands, to access large PGDBs, or just to start up. The data used by Pathway Tools is stored in a location called "the heap". When Pathway Tools is started it tries to reserve one large block of memory for its heap, probably around 700MB. If it cannot reserve this much memory, that value is automatically lowered. In such a case you may see a message of the form
Temporarily scaling back lisp reserved region from x to y byteswhere x should be around 700MB and y is smaller. This is not an error in itself and Pathway Tools should continue to work. Another possible error message is something like
lisp heap being relocated by yyyyy bytesin that case, Pathway Tools is starting up, and this relocation operation -- typically caused by a misconfigured Microsoft DLL -- may take more than a minute. A typical culprit is Service Pack 2 which has a DLL that is not relocatable in memory. This problem should not be fatal, please wait for Pathway Tools to start up. Microsoft provides a hotfix for Service Pack 2, and you will have to contact them to download and install it.
In other cases, you may see an error message of the form
Error: An allocation request for x bytes caused tenuring and a need for y more bytes of heap. The operating system will not make the space available because the address space reserved for the heap could not be increased.The error message may vary, but if it contains the "heap could not be increased", then it is a fatal error and you need to apply one or more of the following remedies. (Please do them in this order)
6. Using the Lisp API
6.1. Setting up Emacs to interact with Pathway Tools in Lisp Mode
Pathway Tools has a built-in Lisp environment that you can use to programmatically query and modify your Pathway / Genome Database. You can access the Lisp listener by starting up Pathway Tools like so:
7. User-Provided Ortholog Data
7.1. I have ortholog data. How do I get it into Pathway Tools?Please see the following link for information on how to load Ortholog data into Pathway Tools.
7. Configuring Pathway Tools
7.1. Configuration for multiple curatorsIf you plan to have multiple curators update a PGDB, there are several possible ways to configure their usage of Pathway Tools.
First, we recommend that each PGDB that will be curated be stored in a single relational database management system (DBMS). Oracle and MySQL are the two DBMSs currently supported by Pathway Tools. All PGDBs can be stored within one DBMS server.
This configuration allows multiple curators to access and update the PGDB in parallel. The Pathway Tools that they run will access the DBMS through network queries.
Curators can run and access Pathway Tools in several possible ways:
7.2. Configuring Proxy Server Access to Circumvent a Firewall for Patch DownloadingSome institutions maintain firewalls, which prevent Pathway Tools from connecting to the WWW server http://bioinformatics.ai.sri.com/ , which is hosting software patches. Because bugs that are reported in between major releases are fixed by issuing patches, it is important that the patches can be downloaded by Pathway Tools, to fix any problems.
These institutions tend to offer an alternate mechanism for WWW access, going through a proxy server. Pathway Tools can download patches through a proxy server, if configured correctly.
To activate proxy server access, the shell environment variable PROXY
has to be set to point to the proxy server and port, prior to
launching Pathway Tools. For UNIX, it is best to do this in one of
the user's shell init scripts such as
setenv PROXY example.hostname.com:8888For MSWindows, right-click on the "My Computer" icon (on the desktop), and choose "Properties". In the window that opens click on the "Advanced" tab, then click on the "Environment Variables" button. In the opened window, under "System Variables" click the "New" button and enter the name and value for the PROXY environment variable.
8. Running multiple instances of Pathway Tools
8.1 Command line arguments to run multiple instances in batch mode w/o using X11Some users want to run multiple instances of Pathway Tools concurrently to do large-scale processing, such as creating many PGDBs with batch PathoLogic. Typically multiple jobs are run in a distributed computing environment. Creation of each PGDB will take 5-15 minutes depending on which inference modules are enabled. It is helpful if the compute nodes have internet access to download the latest Pathway Tools patches, and because some inference modules (such as the Pathway Hole Filler) download data via the internet. If you plan to run multiple Pathway Tools concurrently (typically using PathoLogic), we recommend using the following command-line arguments:
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