Installation instructions for Cyclize.  

1) Prerequisites: 
   Perl v5 or greater - required, free, see http://www.perl.org
   ANSI C compiler    - required, free, see http://www.gnu.org called gcc
   Fortran77 compiler - required, free, see http://www.gnu.org called g77

   Note: 
   1) You do not have to use the gcc and g77 compilers, any ANSI-C 
   compiler and F77 compatible Fortran compiler should work fine.
   2) The F77 compiler is only necessary to compile the ODRPACK fitting
   routines, Cyclize is written completely in ANSI-C.

2) Download the source code:
   The source code is available from ftp://gandalf.bioqmed.ufrj.br/
     in the directory /pub/lapham/software/.  Set the latest version.
   You will find a file named 'cyclize_vX.Y.tar.gz' which represents 
     Cyclize version X.Y.  Save this file in your home directory.
 
3) Uncompress and un-tar the source code:
   Go to the directory into which you would like to install Cyclize:
   `cd /usr/local` (or anywhere, leaving it in you home directory is fine too)

   Uncompress and untar the files there
   `gunzip ~/cyclize_vX.Y.tar.gz`
   `tar xvf ~/cyclize_vX.Y.tar`

   Enter the directory
   `cd cyclize_vX.X`

4) Edit the Makefile
   Find a Makefile.xxx that represents your system (the Makefile.gcc should 
   work on any UNIX system with gcc/g77 installed).

5) Compile the ODRPACK fitting routines
   `make -f Makefile.xxx odrpack.a`

6) Compile Cyclize
   `make all`

7) You must set the CYCLIZE_HOME environment variable
   If you are using a 'csh' derived shell, such as tcsh (place this in your 
   .cshrc file):
   `setenv CYCLIZE_HOME /usr/local/cyclize_vX.Y`

   If you are using a 'sh' derived shell, such as bash (place this in your 
   .bashrc file):
   `export CYCLIZE_HOME=/usr/local/cyclize_vX.Y`

   PS: you may optionally set the CYCLIZE_NICE env variable to a number from
      1-19 which will set the 'niceness' level of your runs.  If you do not 
      set this parameter, the default is 15, which should be okay for most 
      people.

8) READ THE MANUAL!!!!!!!!!!!!!!!!!
   Begin by pointing your web browser to the file html/index.html

------------------------------------------------------------------------------
Test run:

Test the program using the benchmark script.  Return to your home directory 
and make a Cyclize working directory
   `cd`
   `mkdir cyclize`
   `cd cyclize`
   `mkdir bench`
   `cd bench`
   
Copy (and make executable) the benchmark test script
   `cp $CYCLIZE_HOME/html/benchmark/cyclize_bench.pl .`
   `chmod +x cyclize_bench.pl`
   
   Run the script in the background
   `./cyclize_bench.pl >& out &`
   
The script should finish its calculation within 10 minutes 
     (depending on how fast your computer is).  See the manual
	 for more information on comparing the output with a known
	 result, and to see how you machine compares with others
	 in terms of processing time.

Examine the output.
    If you have XMGR installed, enter the subdirectory containing the
    results (cd bench_1) and view the results graphically 
    $CYCLIZE_HOME/perl/show_results.pl

	You may need to edit the file show_results.pl to set the location of 
	xmgr.

