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• CONFIGURATION OF Bio::Das::BioSQL, THE ADAPTER CODE TO BIOPERL-DB
• WARNING
• 1. PREREQUISITES
• 2. CONFIGURING YOUR SYSTEM
• 3. SUPPORT AND BUG REPORTS

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

WARNING

The BioSQL adaptor in its current state is not known to work. Development on this adaptor is ongoing.

1. PREREQUISITES

A) Gbrowse -- http://www.gmod.org/

Make sure that Gbrowse is correctly installed.

B) Bioperl-db -- http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/

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

C) Bioperl-schema -- http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

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

D) Database

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

2. CONFIGURING YOUR SYSTEM

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.

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.

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.

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/

3. SUPPORT AND BUG REPORTS

Please send requests for help to simonf@cshl.edu

Vsevolod (Simon) Ilyushchenko simonf@cshl.edu