Please see the "Requirements" Section in the Pathway Tools Installation Guide.
1. Display Problems 1.1. Motif version: Problems with window resizing, fonts, and breaksQ: 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 PCsQ: 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.
2. Pathway Tools Hang or Freeze 2.1. All-purpose Abort character Control-ZQ: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 GUIQ: 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.
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 inQ: 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 anotherQ: 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.
A: Please see: How to Copy a PGDB Between Computers.
4.2. Importing a .ocelot Format PGDB into Pathway ToolsQ: 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.
4.3. How can I edit or otherwise update PGDBs built 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. See xxx
4.4 Making a copy of a PGDB on one computer (i.e. change the OrgID)Sometimes you want to make changes to a PGDB, yet keep an unmodified copy of the PGDB around, so that you can compare the two versions, such as by running Pathway Tools in web mode, and using the Comparative Analysis tools.
default-version file as found in the external documentation about copying a PGDB from one computer to another.PTOOLS_ORG_ROOTS to include the path where you are placing any newly-copied PGDBs.foocyc to footestcyc.footestcyc/[version]/input/organism.dat file to something unique, such as FOOTEST.NAME & ABBREV-NAME attributes in the same file to signify that they are different than the original. This helps avoid confusion.STORAGE attribute in the same file to be FILE, not MYSQL or ORACLE.footestcyc/[version]/kb directory, and move foobase.ocelot file to footestbase.ocelot .footestbase.ocelot file, and change the :name attribute in the first s-expression (that starts with :OCELOT-KB) to the org-id (from above, FOOTEST) that you selected earlier.footestbase.ocelot file, look for a top-level s-expression that starts a line with (FOO NIL (, where foo is the old org-id. Change it to the new org-id of the copied PGDB (i.e., FOOTEST).foobase, it needs to be replaced with the prefix footestbase. Also, there should be a file with a suffix of .fsa, and a prefix of the Organism ID (i.e., foo). You'll need to change the prefix to the new Organism ID, such as footest.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.
5. Windows (XP, NT, 2000) Specific Problems 5.1. Heap ProblemsThese 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. 8.4. Configuring for off-line, standalone mode (suppressing Internet access) In principle, Pathway Tools can be operated in an off-line manner. However, by default, several types of Internet connections are routinely made, which would have to be disabled. The following is a (mostly complete) listing of connections to services.
For Pathway Tools 27.0 , it should be possible to disable most of the connections described below, by calling the Lisp function (run-in-standalone-mode) . This can be accomplished by supplying the -eval '(run-in-standalone-mode)' commandline argument to the pathway-tools invocation script.
The patches can be downloaded under the following URL: https://bioinformatics.ai.sri.com/ptools/VERSION/PLATFORM/patches/ , whereby VERSION is the release version of the Pathway Tools software. The operating system of the computer, on which Ptools is running, needs to be specified by PLATFORM, and the following choices exist:
An example URL for the 27.0 version of Linux would be this: https://bioinformatics.ai.sri.com/ptools/27.0/Linux-64/patches/
After the patch files have been downloaded, they have to be copied into the patches directory under the Ptools installation directory. The patches directory has a sub-directory, the name of which starts with bin-. The *.fasl patches need to go inside of this sub-directory. An example path for the 27.0 version of Linux would be this: pathway-tools/aic-export/pathway-tools/ptools/27.0/patches/bin-acl-10-1-amd64-linux/
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