# 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
tmp_base = $TMP
persistent_base = $PERSISTENT
userdata_base = $PERSISTENT/userdata
db_base = $DATABASES
# 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 $PERSISTENT/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 $PERSISTENT/sessions.db
# DBI backend to use for uploaded userdata.
# The SQLite option is the easiest to use and the best tested.
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend.
# NOTICE the double semicolon! This is a DBI Perl module, NOT a DBI connection string.
# 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 all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';
# Note the backquotes around the database name, and do be sure to replace "foobar" with
# a more secure password!
# for SQLite
#upload_db_adaptor = DBI::SQLite
# for Berkeleydb
#upload_db_adaptor = berkeleydb
# for mysql
#upload_db_adaptor = DBI::mysql
#upload_db_host = localhost
#upload_db_user = www-data
#upload_db_pass = foobar
# Debug settings
debug = 0
debug_external = 0
debug_plugins = 0
# Performance settings
renderfarm = 1
slave_timeout = 45
global_timeout = 60
search_timeout = 15
max_render_processes = 4 # try double number of CPU/cores
# 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"
# #include "themes/transparent_colors"
# #include "themes/solid_gray_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
track listing style = categories # either "categories" or "facets"
# Loads more details image data than can fit on the screen. This lets the user drag and drop the details
# tracks, without loading more data from the server. A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3
# 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">The Generic Genome Browser. 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 500000 1000000
region sizes = 1000 5000 10000 20000
default region = 5000
fine zoom = 10%
# keyword search maxima
max keyword results = 1000
###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate
####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts = 1
user_accounts_registration = 1
user_accounts_openid = 1
# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.
user_account_db = DBI:SQLite:$DATABASES/users.sqlite
# For SQLite
# user_account_db = DBI:SQLite:$DATABASES/users.sqlite
# For MySQL
# user_account_db = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse
# The number of public files to display
public_files = 10
# 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
#
# here are some common options
# smtp_gateway = localhost # localhost has properly configured outgoing gateway
# smtp_gateway = smtp.oicr.on.ca # indicated machine will forward email for you
# smtp_gateway = smtp.gmail.com:465:ssl:joe.user:secret # use gmail with account "joe.user" and password "secret"
# smtp_gateway = none # disable outgoing email
smtp_gateway = none # disable outgoing email
# 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
######## DEFAULT DATASOURCE #########
default source = yeast
###############################################################################################
# Global settings for plugins (used for the PamAuthenticate plugin only at this point)
###############################################################################################
[PamAuthenticate:plugin]
login hint = your UNIX account
login help = <span style="font-size:9pt">Please see your system administrator for help<br>if you have lost your password.</span>
pam service name = gbrowse
###############################################################################################
#
# DATASOURCE DEFINITIONS
# One stanza for each configured data source
#
###############################################################################################
[yeast]
description = Yeast chromosomes 1+2 (basic)
path = yeast_simple.conf
[yeast_advanced]
description = Yeast chromosomes 1+2 (advanced)
path = yeast_chr1+2.conf
[yeast_renderfarm]
description = Renderfarm demo (gbrowse_slave must be running!)
path = yeast_renderfarm.conf
[pop_demo]
description = Population Display Demo
path = pop_demo.conf
[volvox]
description = Tutorial database
path = volvox.conf