Legal Stuff
-----------

parat 0.9 is (c) 2003 by Sonja Meyer, Arndt von Haeseler, and Lutz Voigt.

The software and its accompanying documentation are provided as is, without
guarantee of support or maintenance. The whole package is licensed under the 
GNU public license, except for the parts indicated in the sources where the 
copyright of the authors does not apply. Please see 

http://www.opensource.org/licenses/gpl-license.html

for details. 


Installation instructions for parat
====================================


For the impatient
-----------------

- Unpack parat.tgz: tar xzf parat.tgz
- Change to the directory parat: cd parat
- Execute the Install shell script and answer its questions: ./Install
- Enjoy



Some more details, please!
--------------------------

Installation of parat is simple. Unpack the archive file parat.tgz in the
desired location. Unpacking the archive yields a directory parat which
contains the shell script Install and the subdirectories src, bin, and .data
(hidden). The src directory contains subdirectories for each of parat' 
programs for the C source files, the bin directory is the location of parat
executables, and .data contains files that parat requires internally. 

Executing the Install script gathers information about special directories, 
compiles the C files in the src-subdirectories, and puts the executable 
programs in the bin-directory. Finally, the parat script is created and 
moved to a directory that is listed in the PATH environment variable.


   Installation instructions (step by step)
   ----------------------------------------

   1. Put the archive file parat.tgz to the directory that should hold the
      parat directory tree, e.g. /my_home_directory/program_packages, open
      a shell and change into the directory with the archive file.
      As mentioned above, unpacking the archive adds the directory parat to
      your current working directory (CWD). If CWD already contains a 
      directory with that name, contents of the archive file are written 
      into this directory. As another consequence, files in that directory 
      might get overwritten. Mentioned this, it is obvious that you should 
      be careful before unpacking the archive...

      Now assuming that you have the GNU tar package installed (see remarks 
      on Requirements) type
	tar xzf parat.tgz
      at the command prompt. 

   2. Change the CWD to /my_home_directory/program_packages/parat, i.e. 
      type
	cd parat

      Attention: parat refers to this directory as its "home place". If you
	ever change the location of the parat directory to another 
	place, you either have to rerun the following steps or (for the 
	brave ones) edit the script files generated during installation 
	process.


      Now that you are ready to start the installation, type
	./Install 

   3. The script file asks for a directory to store the main executable. This
      directory should be listed in your PATH environment variable (i.e. type
      echo $PATH to see its value), so that you can start parat from any
      directory.

   4. Unlucky people, e.g. those who don't have the /tmp directory or are
      not allowed to write to it, are asked for a directory to store 
      temporary files.

   5. To start the program, simply type parat.
      Note: a) Files named rates, rates.old, rates.[integer value], mat,
	       outfile, outtree, ownout, winfile, and SiLiOut in the CWD will 
	       be deleted. Same is true for /tmp/likelihood and /tmp/puzzlein.
	    b) parat is based on an older (modified) version of the treepuzzle
               program that uses a file named infile as input by default. Be
	       sure, that no such file is contained in the CWD. Otherwise
	       rename it or move it to a different location. 


Requirements
------------

Although the parat package is kept as simple as possible, there are still
some conditions that must be fullfilled for installing and running the 
program:

1. Be sure that the GNU tar package is installed. It is required to unzip 
   and unpack the archive file. Alternatively, a combination of gzip/gunzip 
   and anyother tape archiver should work, too.

2. For compiling the C source files one obviously needs a C compiler like 
   GNUs gcc. Furthermore the make program is needed for automisation of the 
   compile resp. install process. 

3. For running the installation script and, later on, the parat program
   package, the bash command interpreter with the dialog extension is 
   required. The latter one takes care of the creation of dialog boxes 
   during excution of the parat shell script. 

4. TCL/TK is required for the graphical user interface.

All of the mentioned programs should be part of any major Linux distribution
(e.g. RedHat, Suse, Debian, ...). Otherwise it is possible to download them
from GNUs FTP server (ftp.gnu.org) resp. www.tcl.tk or one of its mirror sites.