The GAME XML files are usually in /data/shared/ftpsite/tomato_genome/bacs/. I ran this command to collect the ones to load:

cd /data/shared/ftpsite/tomato_genome/bacs/;cp `find . -iregex ".*\.all\.xml" | grep -v unfinished` /home/john/sgn-tools/sgn-db-utils/gbrowse/xml

The command to delete all data from the annotation database is:

./delete_annotation_db.pl cxgn

The command to run to take BAC GAME XML data and add it into the annotation database is this:

./xml2annotation.pl ./xml/*

The command to connect that data to other data in the database (this could be merged into the above script, but right now it isn't) is:

./annotation_foreign_keys.pl

The command to take ALL the data from the annotation database and put it into a GFF text file (run and test this on rubisco) is:

./annotation2gff.pl

The command to take the GFF text file data and use it to recreate the tomato_gff (mysql) database (run and test this on rubisco) is this:

./bp_load_gff.pl --create --user <my_database_username> --password <my_database_password> --dsn tomato_gff tomato_gff.gff

That's it! If that all works, then go to sabazius and do the last 2 steps again (since GBrowse always uses the local mysql database)

TODO: Make an adapter which allows GBrowse to access the data in the annotation database directly. Then the last 2 steps will not be necessary.

--john (john_binns@yahoo.com)