# 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 = $CONF # overridden by environment variable GBROWSE_CONF
htdocs_base = $HTDOCS
url_base = /gbrowse2
db_base = $DATABASES
tmp_base = $TMP
# These paths are relative to the url base
buttons = images/buttons
balloons = images/balloons
openid = images/openid
gbrowse_help = .
js = js
# These paths are relative to the config base
plugin_path = plugins
language_path = languages
templates_path = templates
moby_path = MobyServices
# session settings
session lock type = default
# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver = driver:file;serializer:default
#session args = Directory $TMP/sessions
# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args = FileName $TMP/sessions.db
# DBI backend to use for uploaded userdata.
# The SQLite option is better tested
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend. For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
# mysql> grant create on `userdata\_%`.* to 'www-data'@localhost;
# note the backquotes around the database name.
# for SQLite
#userdb_adaptor = DBI::SQLite
# for Berkeleydb
#userdb_adaptor = berkeleydb
# for mysql
#userdb_adaptor = DBI::mysql
#userdb_host = localhost
#userdb_user = www-data
#userdb_pass =
# Debug settings
debug = 0
debug_external = 0
debug_plugins = 0
# Performance settings
renderfarm = 1
slave_timeout = 45
global_timeout = 60
# Clean up settings (used by the gbrowse_clean script)
expire session = 1M # expire unused sessions after a month
expire cache = 2h # expire cached data if unmodified for >2 hours
expire uploads = 6w # expire uploaded data if unused for >6 weeks
# Appearance settings
truecolor = 1 # better appearance at the expense of larger image files
# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.
#include "themes/warm_colors"
balloon tips = 1
titles are balloons = 1
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper
overview grid = 0
region grid = 0
detail grid = 1
image widths = 450 640 800 1024
default width = 800
pad_left = 60
pad_right = 30
too many landmarks = 100
# where to link to when user clicks in detailed view
link = AUTO
# HTML to insert inside the <head></head> section
head =
# At the top of the HTML...
header =
# At the footer
footer = <hr />
<p style="font-size:small">Generic Genome Browser version 2.00. For questions about the data
at this site, please contact its webmaster. For support of the
browser software <i>only</i>, send email to
<a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a>
or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
</p>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
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
fine zoom = 10%
# keyword search maxima
max keyword results = 1000
####### User Account Registration Database ######
# If "user accounts" is true, then we will try to use
# a user registration database
user accounts = 0
# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.
user_account_db = $DATABASES/users.sqlite
# What email gateway to use for outgoing registration confirmation messages.
# The full format is
# <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
# The port is assumed to be 25 unless ssl encryption is specified, in
# which case it defaults to 465.
# protocol is either "plain" or "ssl", "plain" assumed.
# username and password may be required by the gateway for authentication
smtp_gateway = smtp.gmail.com:465:ssl:authorized_user:authorized_password
# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name = GBrowse
application_name_long = The Generic Genome Browser
email_address = noreply@gmod.org
# name of the "superuser" who can add public tracks
admin_account = admin
admin_dbs = $DATABASES/admin_uploads
###############################################################################################
#
# One stanza for each configured data source
#
###############################################################################################
default source = yeast
[yeast]
description = Yeast chromosomes 1+2 (basic)
path = yeast_simple.conf
[yeast_advanced]
description = Yeast chromosomes 1+2 (advanced)
path = yeast_chr1+2.conf
[renderfarm]
description = Renderfarm demo (gbrowse_slave must be running!)
path = yeast_renderfarm.conf
[pop_demo]
description = Population Display Demo
path = pop_demo.conf