GO-TermFinder version 0.82
==========================

This set of modules can be have been developed under the auspices of
the GMOD project (http://www.gmod.org/), which seeks to create
software that may be generically useful for Model Organism Databases
(MODs).

The latest version of these modules should always be available from:

http://search.cpan.org/dist/GO-TermFinder/

WHAT DO THEY DO?

These modules provide an object oriented set of libraries for dealing
with files produced by the Gene Ontology project (GO -
http://www.geneontology.org/).  In particular, the GO::TermFinder
object allows a client program to provide a list of genes, from which
it will determine p-values for the annotation associated with that
list of genes.  It does this using the hypergeometric distribution.
In addition, a corrected p_value is calculated, to correct for
multiple hypothesis testing.  This distribution also contains a
version of Shuai Weng's GO::View module (and associated classes), such
that you can graphically display the output of the GO::TermFinder.
Some simple clients of these modules are provided in the examples
directory.

INSTALLATION

Firstly, read all the installation instructions before you begin!

To install this software, you will need some limited Unix experience,
and some limited Perl experience.  If in doubt, consult your local
Perl guru or systems administrator.  You also need access to a Unix
machine, such as MacOSX, or a Windows machine running Cygwin, a Linux
box, a Sun machine etc..  Note, that to install the GO-TermFinder
distribution after version 0.70, you need a C++ compiler.  We have
tested installation on MacOSX, Linux, Solaris and Windows (using
Cygwin), all using GCC as the compiler, and everything seems to work.
The Makefile.PL in the native directory is hardcoded to look for g++,
so if you have a different C++ compiler, you will need to edit that
file.  It should give you an error message indicating this, if unable
to find g++.  Thus far, we have not been successful installing under
ActiveState Perl with Microsoft Visual C++, though we have not tried
too hard.  If you can provide a patch for the Makefile.PL that gets it
to work in that environment, we'll happily accept it.

To install the software do the following after downloading the
distribution:

First decompress the gzipped tarfile, e.g:

   tar zxvf GO-TermFinder-0.82.tar.gz

or:

   gunzip GO-TermFinder-0.82.tar.gz
   tar xvf GO-TermFinder-0.82.tar

Then change into the created directory:

   cd GO-TermFinder-0.82

Then actually install it, using the following commands:

   perl Makefile.PL
   make
   make test
   make install

The make install step will require, on most unix systems, that the
command be run with root privileges, as by default it will install the
libraries in a location (usually something like ${PERL5LIB}), which
requires root privileges to write there.  In this case, you would use:

   sudo make install

after which it will prompt you for you sudo password (ask you sysadmin
to do this if you don't have privileges).  If you want to install the
libraries in an alternative place, such as your home directory, which
won't require root privileges, do:

perl Makefile.PL INSTALLDIRS=site INSTALLSITELIB=/home/your/private/dir

as the first step of the installation, where /home/your/private/dir is
your target destination.  Note, for the example scripts to work you
will have to add:

use lib "/home/your/private/dir"

before the other 'use' statements.  Also, during the 'make install'
stage, there will be some complaints about not be able to install man
pages, but you can happily ignore these.

In the case that you get any failures during 'make test', rerun the
tests as 'make test TEST_VERBOSE=1' and send me the full output, and
let me know what version of perl you are using, what compiler and
version you are using, and on what platform you are running.

DEPENDENCIES

This module requires these other modules and libraries:

	Storable   - required for serializing objects to disk
	GD	   - used for creating images in GO::View
	GraphViz   - used for graph layout in GO::View
	CGI        - used by the GO::TermFinderReport::Html object
	Test::More - use for some of the tests

Typically, Storable and CGI will be installed with Perl 5.6 and above.
If you need to find it and install them yourself, you can grab them from:

http://search.cpan.org/dist/Storable/

http://search.cpan.org/dist/CGI.pm/

Test::More is part of the Test-Simple distribution, and is available
here:

http://search.cpan.org/dist/Test-Simple/

GD is available from:

http://search.cpan.org/dist/GD/

Note that installation of the GD module itself has certain
requirements that you must deal with to install it.  GO::View should
be able to work with versions of GD that create png or gif images.

The Perl interface to GraphViz is available from:

http://search.cpan.org/dist/GraphViz/

Note that Graphviz also has some tricky requirements, in that you also
need to install the C version of Graphviz (specifically the dot
binary), as noted in the README for the Perl version of GraphViz.
There are precompiled binaries available for most platforms from :

http://www.research.att.com/sw/tools/graphviz/

On MacOSX, the easiest way to install the C version of GraphViz is to
grab the installer from:

http://www.ryandesign.com/graphviz/

Note, e.g. for version 2.12, this will install the binaries under :

/usr/local/graphviz-2.12/bin/

which the Perl Graphviz won't find, unless you add that to your PATH
environment, or, make a link to the dot binary like:

sudo ln -s /usr/local/graphviz-2.12/bin/dot /usr/local/bin/dot

as /usr/local/bin/ is probably already in your PATH.

You will still need to install the Perl interface to GraphViz manually
though.

Also not, if the graphvic output looks funky, then the versions of the
Perl Graphviz and the dot binary may be incompatible - try updating
both to the latest versions.

The Perl version of GraphViz requires the following modules be installed:

IPC::Run	: http://search.cpan.org/dist/IPC-Run/
Math::Bezier	: http://search.cpan.org/dist/Math-Bezier/
Graph		: http://search.cpan.org/dist/Graph/

and in turn Graph requires:

Heap		: http://search.cpan.org/dist/Heap/

If you do not want to use GO::View, and its client batchGOView.pl
program, then you do not need either GD, or GraphViz.  In that case,
you can comment out their entries in the PREREQ_PM hash in
Makefile.PL, so that installation does not depend upon them.

CONTACT INFO

If you have any suggestions, bug fixes, etc., please send email to
[email protected].

NOTES

The ontology files in the t/ directory are solely for the purposes of
running the test suite.  You should get the latest versions from the
Gene Ontology website (http://www.geneontology.org/) for your own
analyses.

If you seem to be getting some odd behavior that you can't explain,
make sure that the ontology and association files you downloaded from
the Gene Ontology site have not had their line endings converted - the
software is expecting them to be \n, which is what the files have on
the GO ftp site.  It is possible for ftp programs to sometimes mangle
them into control-M's.

COPYRIGHT AND LICENCE (the 'MIT license')

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Copyright (C) 2003-2008 Gavin Sherlock, Stanford University