[SBEAMS-devel] problem with GO install

[<res...@ve...>]

Hi, Eric and Dave -

I have run into a roadblock trying to install the GeneOntology database under MySQL 5.0 on my Linux box.  After a couple of partition-sizing mishaps, I got through Section 1 of the GeneOntology.installnotes (Download and import the Gene Ontology data) in good shape.  In Section 2 (Run gene_annotation scripts in BioLink), however, it seems the scripts are still limited to dealing with a SQL Server database.  For example, processing the first SQL script listed gives this error:

[jhowbert@localhost sbeams]$ $SBEAMS/lib/scripts/Core/runsql.pl --user sbeamsadmin --sfile $SBEAMS/lib/sql/BioLink/BioLink_GOAnnotation_DROPTABLES.sql --database $BIOLINK_DATABASE --delimiter semicolon
Enter password, followed by [Enter] (cntl-C to quit):   
DBD::mysql::db do failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'DROP TABLE gene_annotation
DROP TABLE gene_annotation_type
DRO at /var/www/html/dev1/sbeams/lib/scripts/Core/runsql.pl line 130, <FIL> line 14.

The outcome is the same whether or not I include the --delimiter switch.

The SQL scripts BioLink_GOAnnotation_DROPTABLES.sql and BioLink_GOAnnotation_CREATETABLES.sql are clearly written in the SQL Server dialect.  Have you performed a full GeneOntology install under MySQL?  If so, did you have to do things that are not documented in GeneOntology.installnotes?  Thanks.

Jeff Howbert