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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...
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