=head1 CONFIGURATION OF Bio::DB::Das::BioSQL, THE ADAPTER CODE TO BIOPERL-DB

BioSQL is a Bioperl-based system for storing record-oriented
biological objects, including GenBank/EMBL sequences and PubMed
records, in a relational database. GBrowse provides support for
viewing sequence annotation data stored in BioSQL. The support is
functional, but not heavily tested, so it may still contain bugs.

=head2 1. PREREQUISITES

=over 4

=item A) GBrowse -- L<http://www.gmod.org/>

Make sure that Gbrowse is correctly installed.

=item B) Bioperl-db -- L<http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/?cvsroot=bioperl>

Make sure that you have the latest version of Bioperl-db.

=item C) Biosql-schema -- L<http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/?cvsroot=bioperl>

Make sure that you have the latest version of Bioperl-schema.

=item D) Database 

You need to have a database (MySQL, Postgresql, Oracle) that is supported by the Perl DBI interface.

=back

=head2 2. CONFIGURING YOUR SYSTEM

=over 4

=item A) Create a bioperl database 

If you plan to use MySQL, run create_mysql_db.pl (it is included in
the bioperl-schema distribution). Other databases would use similar
SQL commands.

=item B) Load data into your bioperl database 

Take a Genbank file and call the script load_seqdatabase.pl from the
bioperl distribution to load the data. For example,

   load_seqdatabase.pl --host somewhere.edu --dbname biosql \
                       --namespace bioperl --format genbank \
                       your_genbank_file

The value of "namespace" is arbitrary.

=item C) Configure gbrowse to use bioperl-db

Point a gbrowse configuration file to this database. See include
06.biosql.conf for an example. The only nontrivial parameters in it
are "namespace" and "version". For namespace, use the same value that
you specified when you uploaded data. The version number is contained
in the Genbank file.

=item D) Install the Bio::DB::BioSQL files.

Until these files are uploaded into the bioperl CVS, put the attached
files on your system in a directory accessible to Perl, for example,
into /usr/lib/perl5/site_perl/5.8.1/

=back

=head2 3. SUPPORT AND BUG REPORTS

Please send requests for help to simonf@cshl.edu


Vsevolod (Simon) Ilyushchenko
simonf@cshl.edu
