Bio::Genex -- Perl extension for querying a GeneX gene expression DB
$Id: README,v 1.4 2001/01/26 10:22:04 jes Exp $
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.
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.
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.
Unpack the GeneX distribution tar file anywhere you choose, with a command such as the following:
$ tar zxvf Genex-X.Y.Z.tar.gz
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
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
Jason E. Stewart (jes@ncgr.org || jason@openinformatics.com) Jiaye Zhou (jz@ncgr.org || zebra@inztro.com)
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
Please send bug reports to genex@ncgr.org
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