INSTALLATION
************

This directory contains executables, library files, help files
and an installation script. The purpose of the installation script
is to prompt the user for an installation directory and then to
copy the files to the correct places in that directory.  You
may want to look at the end of this file to see exactly what
files we are putting on your system.

1) First decide if you are going to install the software
   as root or not. 

2) Decide the directory where you are going to install the programs. 
   Decide the directory to put the help files, examples, lib files.

   As root, we suggest a directory such as /usr/local/bds/bin although
   /usr/local/bin is perfectly fine. The only disadvantage to /usr/local/bin
   is that some of the software packages we offer contain alot of
   executables and you may not want us to fill your /usr/local/bin
   directory.

   For the library directory, a good place is /usr/local/lib.

   For non root accounts, we suggest you use $HOME/bds/bin
   as your bin directory  and /bds/lib as your lib directory
   (you can type 'printenv HOME' to get the value of HOME). 

3) Run the install script by typing ./Install.

   The install script then puts the executables in the bin directory
   and everything else will go in the lib directory.

4) Set your path to include the location of the executables. 
   This way you only need to type the name of the program to start it.
   For example, you may want to add a command to your .cshrc similar to
   the one below: 

      set path = ($path /usr/local/bds/bin)

    The first time only, you will need to type "rehash", 
	so that the system can find the programs.


Running the Program
*******************

You can test the program by typing in the program name.
If you have not set up the paths properly, you will need
to give the full path name of the program. 

If the program starts up, then you can read the online
help OR go to the lib/docs directory and use a web browser to
read the html documents (which are nicer). Many of our programs
have example input and output which can be found in lib/examples.

The latest information on our software will be maintained at:

	http://www.pence.ualberta.ca/ftp

Some of our software has expiry dates, you can likely find
new versions at the above web site.


SUN-OS 4.1.X NOTES 
******************

If you have X11 installed on your system then you shouldn't
have any problems. Just make sure that you have defined your
library path to include where your X11 is installed. eg, 

	setenv LD_LIBRARY_PATH /usr/X11R5/lib:/usr/lib 

If you don't have X11, hmm... 


XALIGN FILES INSTALLED
**********************

Here are the files which are being added to your system
by the Install script in order to run xalign:

bin
	xalign: top level script for setting environment and call xalign
	xalign.exe: gui executable written in tcl/tk
	xalign_x: low-level executable (alignment program in c)

lib/xalign

	app-defaults: system Xdefaults for this specific application
	examples: example data and output
	docs: documentation in html and/or help files 

	xalign.parms: default variable parameters for the program
	wtm.rbo: default amino acid scoring matrix