Instructions for Converting a GFF3-Based GBrowse Installation to Run Using a MySQL Backend to Speed Up Data Retrieval

(Assumes Bioperl/GBrowse/Mysql/Apache are already installed on Ubuntu, and the GBrowse installation currently has its data stored in GFF3 flat files)

Create a new Mysql database

 % mysql -u root -p -e 'create database new_database_name'

Run Bioperl conversion script (substitute your new database name, Mysql root user password, GFF data directory name, and all GFF/Fasta filenames)

 % mkdir /home/$USER/tmp-load
 % cd /var/www/gbrowse/databases/my_current_GFF_data_directory
 % sudo bp_seqfeature_load -d new_database_name --user root --password my_password \
 --create --T /home/$USER/tmp-load --verbose \
 seq.gff \
 pfam.gff \
 blastp.gff \
 genemark2.4.gff \
 glimmer.gff \
 tmhmm.gff \
 readcoverage.gff

 % rm -rf /home/$USER/tmp-load

Add privileges to the database (substitute your db root password, new database name, and your login username)

 % mysql -u root -p root_password -e 'grant all privileges on new_database_name.* to my_username@localhost;
 % mysql -u root -p root_password -e 'grant file on *.* to my_username@localhost;
 % mysql -u root -p root_password -e 'grant select on new_database_name.* to 'www-data'@localhost;

Create a new GBrowse configuration file by copying your existing file (substitute your existing file and new database name)
```
 % cd /etc/apache2/gbrowse.conf
 % cp existing.conf new_database_name.conf
```
Edit the new GBrowse configuration file (substitute your new database name)–

Use the right database adapter by putting the following lines at the beginning of the file:
```
 db_adaptor    = Bio::DB::SeqFeature::Store
 db_args       = -adaptor DBI::mysql
 -dsn dbi:mysql:database=new_database_name
```
Restart Apache
```
 % sudo apache2ctl restart
```
Browse to the new site, and check the checkboxes or click the “Configure Tracks” button to do your initial layers/view setup
```
 http://localhost/cgi-bin/gbrowse/new_database_name/
```