The BioSQL adaptor in its current state is not known to work. Development
on this adaptor is ongoing.
- 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.
- 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/
Please send requests for help to simonf@cshl.edu
Vsevolod (Simon) Ilyushchenko
simonf@cshl.edu