Last updated: gilham:Oct-21-2009
0. What are the system requirements -- hardware and software -- to use Pathway Tools?
Please see the Section "Requirements" in the Pathway Tools Installation Guide at here.
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
library libXm.so.2 . Make sure that
libXm.so.2 (located in either /usr/lib or
/usr/X11R6/lib ) points to the OpenMotif version, not
Lesstif.
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
http://www.opengroup.org/openmotif/ .
The version with the most bug fixes appears to be metrolink/openmotif-2.1.30-4_MLI.i386.rpm .
After installation, if you end up having both
libXm.so.2 and libXm.so.3 , you probably
need to delete the Lesstif libXm.so.2 , and make a
symbolic link from libXm.so.3 to libXm.so.2
( ln -s libXm.so.3 libXm.so.2 ).
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 libXm.so.2 but the OpenMotif
installation does not have that particular version link, please try to
make a symbolic link to "fake" that version, to see whether that will
work. Some variation of this example should do it (you will need to
be the root user):
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.
1.2. X-Display Emulation on Microsoft Windows PCs
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.
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.
1.4. Colormap and interference by Netscape browser
Q: The Unix Pathway Tools displays an error message saying it is unable to allocate or display certain colors -- what do I do?
A: This problem usually occurs because the colormap on the display
host is full, which is often caused by the Netscape program (a known
color hog). Primarily, this will occur with video card graphics
settings that allocate only 8 bits to color. It is best to allocate
24 bits to the color depth. If this is not possible, to work around
the problem, exit from Netscape and then restart the Pathway Tools. If
you wish to run Netscape concurrently with the Pathway Tools, invoke
Netscape using the command
netscape -install
which instructs Netscape to use a separate colormap, or invoke it
with a limited number of assigned colors like this
netscape -ncols 100 .
2. Pathway Tools Hang or Freeze
2.1. All-purpose Abort character Control-Z
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.
2.2. Unresponsive GUI
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:
Restart actions (select using :continue): 0: Return to Pathway Tools command level 1: Pathway Tools top level 2: Exit Pathway Tools [changing package from "USER" to "ECOCYC"] [1] EC(3):The software is in a state called a "break" and you are interacting with a debugger. You can probably resume operation by typing :continue followed by the number of the line on which the text "Pathway Tools top level" occurs. In the case shown here you would type :continue 1 followed by Return.
If restarting did not work, try typing (exit) to exit from the Pathway Tools (if you exit, you will lose any KB updates in the current session that you have not already saved; to attempt to save those changes, type (save-kb) before typing (exit)). You will now be back to the operating system, and you can execute the Pathway Tools anew.
3. Running the Pathway Tools as a WWW Server
3.1. Graphics do not get generated
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
directory.
3.2. Running server without staying logged in
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.
4. PGDB Maintenance
4.1. Copying PGDBs from one computer to another
Q: How does one copy a file PGDB, for example from one computer to another ?
A: Please see: How to Copy a PGDB
Between Computers.
4.2. Can I update PGDBs that are built into Pathway Tools?
Q: Can I update PGDBs that are built into Pathway Tools?
A: "Built-in" PGDBs are physically included within Pathway Tools when it is downloaded from SRI. These PGDBs should not be updated because the updates cannot be saved, and if they were to be saved, they could not overwrite the built-in versions of each PGDB.
If you want to update one of the BioCyc PGDBs available from SRI,
please contact
.
SRI will send you file versions of these PGDBs, which must be used in
conjunction with the Pathway Tools configuration that contains only
the EcoCyc and MetaCyc PGDBs.
4.3. Retaining Locally Created PGDBs Across New Pathway Tools Versions
Q: How can I be sure a PGDB I have created is retained when I install a new Pathway Tools version ?
A: There are two Pathway Tools software releases per year.
Users who have built a PGDB using a prior version of Pathway Tools
and who want to upgrade the software will usually want to retain
that PGDB. As of version 10.0 of Pathway Tools, retaining locally created PGDBs became
trivial because they are now kept in a directory called ptools-local that
is outside the directory containing Pathway Tools itself, and that is unaffected
by new Pathway Tools installations.
Do be aware that when installing a new version of Pathway Tools, the schema of your old PGDB must be upgraded to be compatible with the new software, at which point it will become incompatible with the old version of the software. Through version 10.0 of Pathway Tools, we suggest you back up your PGDB before performing the upgrade because the upgrade will overwrite the existing version of your PGDB; the upgrade is performed using the command Tools->Upgrade Schema of Current PGDB. After version 10.0, the software will upgrade the schema automatically the first time the PGDB is opened under a new version of the software, and will also create a new version directory for the PGDB so that its previous version is retained.
If the new Pathway Tools version is to be installed on a new
computer, then existing PGDBs can be copied using e.g. a Tar file.
4.4. 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 wish to programmatically access the data, you should use one of our Lisp, Perl or Java APIs instead.
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.
4.5. Importing a Flat-File PGDB into Pathway Tools
Q: How do you take a PGDB downloaded from the BioCyc website, and import it into Pathway Tools?
A: Please see: How to Import a Flat-File PGDB into Pathway Tools.
4.6. Why can I not edit any of the PGDBs in Pathway Tools?
All of the PGDBs that are "built-in" to the Pathway Tools runtime (Tier 1 always, and Tier 2 & Tier 3 depending on which runtime that you downloaded) are not editable.
As per our Installation Guide: "If editable PGDBs are needed, a distribution containing only Tier 1 (and possibly Tier 2) should be chosen, and the PGDBs to be edited should be downloaded from the Registry. " Any PGDB that you either build yourself, get from someone as a flat-file copy, or from the Pathway Tools Registry will be editable.
If you let us know what combination of PGDBs you'd like to be able to edit, we can help you determine your best combination of software and PGDB downloads.
5. Windows (XP, NT, 2000) Specific Problems
5.1. Heap Problems
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)
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: pathway-tools -lisp. Interacting with it via Emacs provides you with a fully-integrated IDE that provides debugging support, syntax high-lighting, and syntax-aware navigation commands. The recommended Common Lisp interaction platform for Pathway Tools users is SLIME, the Superior Lisp Interaction Mode for Emacs.
These instructions were generously provided by Jeremy Zucker.
.emacs file:
(setq slime-lisp-implementations
'((ptools ("/usr/local/bin/pathway-tools" "-api" "-lisp") :init slime-init-command)))
(add-to-list 'load-path "/path/to/slime")M-x slime, you will get an error like this:Condition: Can't locate the module "SCM"files.bu into the pathway-tools exe directory (shown below).cp /Applications/AllegroCL/files.bu /usr/local/pathway-tools/aic-export/pathway-tools/ptools/12.5/exeFirst, 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:
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 .cshrc or
.login. As an example, in csh syntax:
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.