Bio::Genex -- Perl extension for querying a GeneX gene expression DB

   $Id: README,v 1.3 2001/01/14 22:00:06 jes Exp $

LEGAL HOOP JUMPING
==================

Copyright (c) 2000 National Center for Genome Resources. 
All rights reserved.  

This package is free software. It is distributed under the terms of
the Lesser GNU Public License (see LICENSE for details).

The authors of this software make no claims as to the performance or
reliability of this product. Use it at your own risk. If you find it
helpful, We're very happy for you, if not, don't hold us responsible.

WHAT
====
This module provides a perl API to NCGR's GeneX gene expression DB. It
provides a number of classes for manipulating expression data in a
genex database, helper utilities, and example code. Please see the
doc/ subdirectory for more information.

PREREQUISITES
=============
This module requires the following other Perl modules not included
with the statndard distribution:

   CGI      - used by most cgi scripts
   XML::DOM - used by the GeneXML utils
   DBI      - used by everything (this *is* a gene expression DATABASE ;-) 
   DBD::Pg  - for the default Postgres installation
   GD       - (optional, currently only used by draw-map.pl)

These modules must be installed *before* attempting to install
Genex.pm. They can be installed individually, or by installing
Bundle::Genex. 

INSTALL
=======

Unpack the GeneX distribution tar file anywhere you choose, with a
command such as the following:

   $ tar zxvf Genex-X.Y.Z.tar.gz

Perl
----
To install this package you need perl5.005 or later

Best place to get the laterst version of perl is via 'CPAN' site
nearest you

   $ ftp any-CPAN-site 
   $ cd CPAN/src/5.0
   $ bin
   $ get current.tar.gz

If you have perl5.005 or later installed in the normal way you proceed
with configuring Genex

Congiguring
-----------
For Genex.pm to be useful, you must have already installed a working
GeneX server on your system. In order for Genex.pm to properly
configure itself, it must find the Genex/Config.pm that was installed
with the rest of the GeneX perl modules. Since the Genex/Config.pm was
likely installed in the private Genex lib directory, you will need to
be sure that it is in your Perl lib path. To ensure this, include the
GeneX lib dir in your PERL5LIB:

   $ export PERL5LIB=/var/lib/genex/perl5:$PERL5LIB

Substitute in the proper directory for /var/lib/genex/perl5

As with most perl modules the next step is:

   $ perl Makefile.PL

This will use the Genex/Config.pm to determing the installation
information that is necessary for GeneX to run properly on your
machine.

After configuration, run the regression tests to see if things were
configured properly

   $ make test 

Finally, if all looks good, install it.

   $ make install

RUNNING
=======
After installing the package, you should be able to investigate the DB
with the following URL's (just substitute in the values that you
supplied for CGIURL and WWWHOST for your installation).

  http://$WWWHOST/$CGIURL/genex/samples/query-intro.pl

AUTHOR INFO
===========
Jason E. Stewart (jes@ncgr.org || jason@openinformatics.com)
Jiaye Zhou (jz@ncgr.org || zebra@inztro.com)

SEE ALSO
========
For more general information about the GeneX system:

http://genex.ncgr.org/         -- the NCGR GeneX home page

http://genex.sourceforge.net/  -- the GeneX distribution home page

BUG REPORTS
===========
Please send bug reports to genex@ncgr.org


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