This is the README file for TFBS modules distribution,
Version 0.3.0


*NOTE* 

 Much of this README file has been copypasted and adapted from 
 bioperl distrubution README file. Sorry, guys, but you've done such
 a great job that I just could not ignore it :)


o About TFBS

 TFBS is a computational framework for transcription factor binding site
 analysis. It can also be used for analysis involving other DNA paterns
 representable by matrices, e.g. splice sites. 


o Contact info

 Author: Boris.Lenhard@cgb.ki.se

 TFBS website   : http://forkhead.cgb.ki.se

 Bug reports       : contact author

 Please send bug reports, in particular about documentation which you
 think is unclear or problems in installation. The author is also 
 interested in suggestions on directions in which TFBS functionality
 should be expanded.


o System requirements

 - Tested only on Linux/i686, Tru64 Unix, Solaris
 - perl 5.005_03 or later.
 - ANSI C or Gnu C compiler for XS extensions
 - bioperl 0.7.* 
   (use the TFBS-0.3.0.DEV distribution with bioperl 0.9.*)
 - Additional perl module and application dependencies listed at
   http://forkhead.cgb.ki.se/TFBS/



o Documentation

 The modules have a reasovably complete POD documentation. 
 After instalation, type e.g.

      perldoc TFBS::Matrix::ICM

 to display the documentation for a particular module.

 POD documentation for all modules, as well as additional 
 information can be accessed from TFBS web page at
 http://forkhead.cgb.ki.se/TFBS/ .

 A limited amount of example code, can also be found in the 
 examples/ directory. The current collection includes scripts for 
 demonstrational purposes. The explanations an be found in the source
 code of individual scripts.


o Releases
  
 
 The 0.9.x developer series releases are intended to be quick
 releases off the main trunk to provided FTPable code that has been
 test that it will compile and all tests pass reasonably.  In the
 future all odd numbered point releases will be developer releases and
 even point releases will be stable releases.


o Installation


 The TFBS modules are distributed as a tar file in standard perl
 CPAN distribution form. This means that installation is very
 simple. Once you have unpacked the tar distribution there is a
 directory called TFBS-xx/, which is where this file is.  Move into
 that directory and
 issue the following commands:

   perl Makefile.PL   # makes a system-specific makefile
   make               # makes the distribution
   make test          # runs the test code
   make install       # [may need root access for system install.
                      #  See below for how to get around this.]

 This should build, test and install the distribution cleanly on your
 system, provided that all prerequisite modules have been installed.
 Running perl Makefile.PL will ask you for a MySQL server write access 
 details if you want to test TFBS::DB::JASPAR2 module. You can safely
 choose not to do the test by answering "no" tho the first questions.

 To install you need write permission in the perl5/site_perl/ source area. 
 Quite often this will require you (or someone else) becoming root, 
 so you will want to talk to your systems manager if you don't 
 have the necessary access.

 It is possible to install the package outside of the standard Perl5 
 location. See below for details.


 INSTALLING TFBS IN A PERSONAL OR PRIVATE MODULE AREA

 If you lack permission to install perl modules into the
 standard site_perl/ system area you can configure TFBS to
 install itself anywhere you choose. Ideally this would
 be a personal perl directory or standard place where you
 plan to put all your 'local' or personal perl modules. 

 Note: you _must_ have write permission to this area.

 Simply pass a parameter to perl as it builds your system
 specific makefile.

 Example:

   perl Makefile.PL  PREFIX=/home/borisl/perllib
   make
   make test
   make install

 This will cause perl to install the TFBS modules in:
 /home/borisl/perllib/lib/perl5/site_perl/

 And the man pages will go in:
 /home/dag/My_Perl_Modules/lib/perl5/man/

 To specify a directory besides lib/perl5/site_perl, 
 or if there are still permission problems, include
 an INSTALLSITELIB directive along with the PREFIX:

   perl Makefile.PL  PREFIX=/home/borisl/perl INSTALLSITELIB=/home/borisl/perl/lib

 See below for how to use modules that are not installed in the
 standard Perl5 location.



 USING MODULES NOT INSTALLED IN THE STANDARD PERL LOCATION

 You can explicitly tell perl where to look for modules by using the
 lib module which comes standard with perl. 

 Example:

    #!/usr/bin/perl -w

    use lib "/home/borisl/perllib/";
    use TFBS::PatternGen::Gibbs;

    # etc...
