ACeDB - Installing the Pathway Database

If are not already familiar with what ACeDB is and how it works, you should really go through one of the tutorials BEFORE trying to install this package.

I recommend
Tutorial Introduction to ACEDB
by Bruno Gaëta Australian National Genomic Information Service

Now, you are ready to install the database.

Install the sample database


Download the sample ACeDB database (pathways.tar.Z, 65k)

Uncompress the file:

uncompress pathways.tar.Z

Unarchive the .tar file:

tar xvf pathways.tar

This will create a directory called 'pathways', containing the following files and subdirectories:

drwx------   2 psgendb  psgendb      512 Mar 22 00:05 bin/
drwx------   2 psgendb  psgendb      512 Mar 22 00:07 database/
drwx------   2 psgendb  psgendb      512 Mar 21 23:26 externalFiles/
-rw-------   1 psgendb  psgendb     2766 Mar 22 12:44 pathways.ace
lrwxrwxrwx   1 psgendb  psgendb       25 Mar 28 19:16 whelp -> /home/psgendb/acedb/whelp/
drwx------   2 psgendb  psgendb      512 Jun 13  1997 wspec/

bin - shell scripts for running your copy of ACeDB. Does NOT contain the ACeDB binaries!
database - empty directory. This is where the binary database file will be created
pathways.ace - An .ace file in ASCII text that can be read and edited in any text editor. This file can be read in by ACeDB to create the pathway database. See below for details.
externalFiles - Image and GenBank files that can be viewed using ACeDB.
wspec - Parameter files read by ACeDB at run time. These files contain class definitions and parameters affecting things like the size of the database and and which classes appear in the main window.

Download the ACeDB executables

If a copy of xace is already on your system in a world-readable directory, skip this step. BIRCH users at the Univ. of Manitoba, THIS MEANS YOU!

Download the Solaris2 executable files (ftp://ftp.cc.umanitoba.ca/psgendb/labace.bin.solaris.tar.Z, 2.6Mb)

Uncompress the file:

uncompress labace.bin.solairs.tar.Z

Unarchive the .tar file:

tar xvf labace.bin.solaris.tar

This will create a directory called 'labace.bin', containing the following executable files:

-rwx------   1 psgendb  psgendb  1115432 Jun 12 18:34 tace*
-rwx------   1 psgendb  psgendb  4054312 Jun 12 18:34 xace*

tace - text-based ACeDB program
xace - X-windows ACeDB program
Move these files to a directory that is readable by all your intended users. That could be pathways/bin, or some other directory in which

If you are not on a Sun Solaris 2 system, you must download the executbles from other ACeDB sites. The only files you need are xace and tace. The Download the whole .tar.Z file, copy these files to a world-readable directory, and delete all the rest of the files and directories.

Download ACeDB for non-Solaris platforms. (http://probe.nalusda.gov:8000/acedocs/whereacedb.html)

Set up the sample lab database

• The file pathways/bin/pathace is the script that runs xace, the ACeDB program. This script sets several environment variables that tell xace where to find files. Change the environment variable ACEDB to your pathace directory eg.

setenv ACEDB $HOME/pathways

I have found that these paths must be fully qualified eg. pathace wasn't accepted by the program. The environment variables ACE_XEditor and ACE_Viewer hold the names of programs that are used by xace to view ASCII text files or graphic files, respectively. By default, pathace uses Sun's textedit as the editor and the freeware program xv as the graphics viewer. If these are not already set when pathace is called (eg. you set them in you .cshrc file), then pathace will set them. You may specify a default by changing the setenv statements in pathace, and each user could, if desired, override those settings in their .cshrc files. Finally, pathace uses these two environment variables to build the environment variables ACE_EDIT_COMMAND and ACE_VIEW_COMMAND. These two variables contain a call to the script ACErunexternal. All ACErunexternal does is to create a copy of the file (from pathace/externalFiles) in the directory in which pathace was launched, and then opens that file up in the editor or viewer. That way, if the user wishes to save a copy of the file, they are already in their own directory, rather than in pathace/externalFiles.
• To be database administrator, you need to put your userid into wspec/passwd.wrm. Anyone who is supposed to have write permissions must have their userid in this file. At the end passwd.wrm are the following lines:
  
  // Login name of the administrator installing acedb 
  psgendb
  
  Change 'psgendb' to your Unix userid.
  
  
  
• pathace must be in your PATH. Usually, one's path is set in the $home/.login file. The command setting the current path may look something like this:

 

set path = ($path $home/bin)


Change the path to include the pathace/bin directory. It is usualy best to add new directories to the end of the existing path.
 

set path = ($path $home/bin $home/pathace/bin)


You must logout and log back in to make this change take effect.

If you want to omit this step, you will have to cd into your pathways directory and type 'bin/pathace' each time you run the program.
 

• Now we're ready to try out pathace. Initially, the database will be empty, and we can build a database from the user-readable dump file.  To start ACeDB, type

pathace

and a message window will pop up, telling you that ACEDB.wrm does not exist, and asking if you wish to reinitialize the system. Click 'Yes'. Two more popup windows will tell you that database.wrm and subclasses.wrm do not exist. Click on 'Continue'. Finally, two windows should appear, the main ACEDB window and the Main Keyset. The ACEDB window is shown below:



Initially, the database is empty, but you can recreate a test database by reading in the dump file present in the pathace directory.

First, we need write access. Click on the Edit button to bring up the edit menu



Now, clidk on "Gain write access to gain write access. If it doesn't let you have write access, it is probably because you haven't added your userid to wspec/passwd.wrm. A "Save" button will appear in the main window.

You can also access menus from the Main window by holding down the right mouse button over a menu button.  Hold down the right mouse button over the Edit button, and choose  'read .ace files' from the popup menu.   The .ace file parser window will pop up.


Click on "Open ace file" and the following window will appear:


Click on "pathways.ace, and that name will be copied into the yellow "File" field, as shown in the figure. Click on Ok, and then return to the .ace file parser window. Click on "Read all" and ACEDB will read in the .ace file. At the end, 56 items should be listed, with 0 Errors. If errors were to appear at this point, they would be listed one by one, with line numbers in the .ace file. Using the line numbers as a guide, you can go into the .ace file and correct errors. This is very useful to know as you create your own databases. To dismiss the .ace file parser window, hold down the right mouse button over this window and choose 'Quit'.

You have now successfullly re-created an ACeDB database. This is exactly the procedure you will follow if you create your own .ace files.

Before going any further, save your database by going to the main ACEDB window , holding down the right mouse button, and choosing 'Save'.

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