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 ### *** emacs file mode definition *** ### Local Variables: ### mode:text ### mode:filladapt ### End: