# internal documentation on how to set up a 
# Gbrowse in Goettingen
# to display predictions from the AUGUSTUS pipeline
# Mario, 12.6.2009

ssh mario@gbrowse-web

cd /srv/apache2/conf/gbrowse.conf
su
touch /srv/apache2/conf/gbrowse.conf/chlorella.vulgaris.conf
chown mario:webservd chlorella.vulgaris.conf
exit

# adjust config file with editor
xemacs -nw chlorella.vulgaris.conf

# for flatfiles with tracks:
mkdir /srv/apache2/htdocs/gbrowse/databases/chlorella.vulgaris

scp -C /c1/scratch/mario/chlorella.vulgaris/chlorella.vulgaris21814/gbrowse/* mario@gbrowse-web:/srv/apache2/htdocs/gbrowse/databases/chlorella.vulgaris/

follow docu in GBROWSE tutorial:
19. Setting up a MySQL database

mysql -uroot -p
create database chlorella_vulgaris;
# beware: do not use a '.' in the database name
grant all privileges on chlorella_vulgaris.* to mario@localhost;
grant select on chlorella_vulgaris.* to nobody@localhost;
quit

# load into database
# first clean database (-c)
bp_load_gff.pl -c -d chlorella_vulgaris

cd /srv/apache2/htdocs/gbrowse/databases/chlorella.vulgaris/
bp_load_gff.pl -d chlorella_vulgaris *.gbrowse *.fa *.gff

# then surf on 
http://gbrowse.gobics.de/cgi-bin/gbrowse/chlorella.vulgaris/

