# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries
[GENERAL]
config_base = ./testdata/conf
htdocs_base = ./testdata/htdocs/gbrowse
url_base = /gbrowse
db_base = ./testdata/data
tmp_base = /tmp/gbrowse_testing
tmp_slave = /tmp/gbrowse_testing
# These paths are relative to the url base
buttons = images/buttons
balloons = images/balloons
gbrowse_help = .
js = js
# These paths are relative to the config base
plugin_path = ../../../conf/plugins
language_path = languages
templates_path = templates
moby_path = MobyServices
userdb_adaptor = auto
# session settings
session driver = driver:file;serializer:default
session args = Directory /tmp/gbrowse_testing/sessions
# turn off annoying warnings!
generate pdf = 0
# Debug settings
debug = 0
debug_external = 0
debug_plugins = 0
# Performance settings
renderfarm = 1
global_timeout = 60
remember_source_time = +3M
remember_settings_time = +1M
url_fetch_timeout = 5
url_fetch_max_size = 1000000
expire cache = 2h
# Appearance (can be overridden in per datasource config files)
# the stylesheet is relative to url_base if not otherwise noted
stylesheet = gbrowse.css
plugins = FastaDumper RestrictionAnnotator SequenceDumper
overview bgcolor = lightblue
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
show track categories = 0
image widths = 450 640 800 1024
default width = 800
# HTML to insert inside the section
head = sub { 'this is a subroutine' }
# At the top of the HTML...
header =
# At the footer
footer =
$Id: GBrowse.conf,v 1.15 2009-05-14 21:46:09 lstein Exp $
# Various places where you can insert your own HTML -- see configuration docs
html1 = This is inherited
html2 =
html3 =
html4 =
html5 =
html6 =
# Limits on genomic regions (can be overridden in datasource config files)
region segment = 200000
max segment = 5000000
default segment = 5000
zoom levels = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 5000000 1000000
region sizes = 1000 5000 10000 20000
default region = 5000
# keyword search maxima
too many segments = 5000
too many features = 100
too many refs = 5000
max keyword results = 1000
# constants you probably don't need to change
mag icon height = 20
mag icon width = 8
fine zoom = 10%
tiny seg size = 2
expand seg size = 5000
overview ratio = 1.0
annotation edit rows = 25
annotation edit cols = 100
###############################################################################################
#
# One stanza for each configured data source
#
###############################################################################################
default source = volvox
[yeast_chr1]
description = S. cerevisiae chromosome I
path = yeast_chr1.conf
[volvox]
description = Volvox Example Database
path = volvox_final.conf