# 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 slave_timeout = 45 global_timeout = 60 search_timeout = 15 max_render_processes = 4 # try double number of CPU/cores preload data sources = 0 # when true & f[ast]cgi loads all datasources at startup, # can be bad if many or ds have many tracks # Renderfarm settings #include renderfarm.conf # 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 # truetype = 1 # turn on vector fonts in tracks. Requires Bio::Graphics 2.33 or higher, and truetype support on the server. # 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 section head = # At the top of the HTML... header = # At the footer footer =

The Generic Genome Browser. For questions about the data at this site, please contact its webmaster. For support of the browser software only, send email to gmod-gbrowse@lists.sourceforge.net or visit the GMOD Project web pages.

# 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 # :::: # 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 = Please see your system administrator for help
if you have lost your password. 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