/usr/share/doc/augustus/pipeline2gbrowser.txt is in augustus-doc 3.3+dfsg-2build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | # 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/
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