Revision as of 17:51, 11 December 2008

Introduction

GBrowse 2.0 is a complete rewrite of the original GBrowse version. In addition to making the code base more maintainable, GBrowse 2.0 adds the following major features:

• User Interface: The user interface uses AJAX to provide a smoother user experience. Tracks turn on and off immediately, and updates affect only the tracks that have changed.

• More rational configuration: Most configuration options have been moved into a single shared configuration file. This allows data source-specific files to be shorter and more concise. This also increases the performance for sites that use hundreds of configuration files to display annotations on multiple species because only the global configuration file and the source-specific configuration file need to be read.

• Multiple database support: You can now declare multiple databases for each data source and attach them to different tracks. This allows you to add and remove genome annotation data sets far more easily than in earlier versions.

• Slave renderer support: If you have a multi-CPU processor, or access to several machines, you can distribute the tasks of reading the databases and rendering tracks across multiple processes and machines via a series of "slave" renderers. This greatly increases performance.

This document describes how to install and configure GBrowse 2.0 on your system. Readers familiar with GBrowse 1.70 or earlier should start with the next section, which is a quick summary of what is different. Readers who have not installed or configured GBrowse before should skip to GBrowse Installation.

For Users of GBrowse 1.X

GBrowse 2.0 is largely backward compatible with GBrowse 1.X, but you will need to do some modest work in order to port existing sources to the new system. Please see Migrating from GBrowse 1.X to 2.X for a guide to the process.

GBrowse Installation

This section describes how to install GBrowse 2.0 on either Linux or Mac OSX systems. Windows users please see Installing GBrowse 2.0 on Windows (document pending).

Prerequisites and Downloading

First, make sure that your system has all the GBrowse 2.0 Prerequisites installed.

Download (or CVS checkout) the distribution. GBrowse 2.00 is currently only available via CVS, so the command to issue is:

cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co Generic-Genome-Browser

This will create a directory named Generic-Genome-Browser:

Running the Build.PL Script

Next, enter the newly-created directory and run the Build.PL script:

 % '''cd Generic-Genome-Browser'''
 % '''perl Build.PL'''
 Checking whether your kit is complete...
 Looks good

 Checking prerequisites...
 Looks good

 cc -I/usr/lib/perl/5.8/CORE -fPIC -c -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o /tmp/compilet.o /tmp/compilet.c
 cc -shared -L/usr/local/lib -o /tmp/compilet.so /tmp/compilet.o

 Creating new 'Build' script for 'GBrowse' version '2.00'
 Now run:
  ./Build test
  ./Build config
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

% cd ~/packages
% wget http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz
% tar zxvf bioperl-live.tar.gz
% cd ~/packages/Generic-Genome-Browser
% perl -I ~/packages/bioperl-live Build.PL

Among other things, this script will check for missing Perl libraries that you need to run GBrowse, and will tell you about them. Please be sure to install all prerequisites before going any further. All but one of the prerequisites can be downloaded from CPAN or installed from the command line using the CPAN shell. There are also Debian and RPM installer packages for these libraries. See GBrowse 2.0 Prerequisites for full details.

This will create a script named Build in the current directory.

Running the Build Script

You will now use Build to test, configure and install GBrowse. First you will confirm that GBrowse's libraries are completely functional by running ./Build test (the "./" is there to ensure that you are running the Build script in the current directory, and not some other Build script somewhere in your path:

 % '''./Build test'''
 t/01yeast...................ok
 t/02.rearchitecture.........ok
 t/03.render.................ok
 ...
 All tests successful.
 Files=8, Tests=323, 12 wallclock secs
 Result: PASS

All tests should pass (you may safely ignore warnings and occasional timeout errors). If not, please file a bug report, and/or send an inquiry to the GBrowse mailing list.

Selecting Installation Directories

After passings its tests, you should configure GBrowse by running ./Build config:

 % '''./Build config'''

 **Beginning interactive configuration**
 Apache loadable module directory (for demo)? [/usr/lib/apache2/modules]
 Apache CGI scripts directory? [/usr/lib/cgi-bin]
 Directory for GBrowse's config and support files? [/etc/GBrowse2]
 Directory for GBrowse's static images & HTML files? [/var/www/gbrowse2]
 Internet port to run demo web site on (for demo)? [8000]
 User account under which Apache daemon runs? [www-data]

 **Interactive configuration done. Run './Build reconfig' to reconfigure**

The configuration process will ask you to confirm six site-specific configuration options, and will do its best to guess for you. In most cases you can just hit return to accept the default. If you specify a directory that does not exist, the system will ask you to confirm that this is what you mean. If you press yes, the directory (and all its needed parents) will be created at install time.

The configuration options are:

apachemodules

The directory in which Apache's loadable modules are located. This is only needed to run a demo GBrowse site before formal installation. If you do not know the location of this directory and you do not want to run the demo, you can safely ignore this option.

cgibin

The directory in which Apache's executable CGI scripts are located, for example /usr/lib/cgi-bin. This directory is set up for you when Apache is installed, and you must have the path correct in order for Build to install GBrowse's CGI scripts in the right place. GBrowse will be installed into the "gb2" subdirectory, so its path will be "/usr/lib/cgi-bin/gb2/gbrowse".

conf

The location of GBrowse's configuration files. The default is to place them in /etc/gbrowse2. This is where you will go to customize GBrowse and add new data sources.

databases

The default location for GBrowse's in memory databases, and the place where the example databases will be stored. The default is to place this into a subdirectory of the same directory in which GBrowse places its static files, such as /var/www/gbrowse2/databases.

htdocs

The directory in which to install GBrowse's Javascript libraries, static HTML pages and stylesheets. You can choose any location for this directory and it will be added to Apache's document tree. The default is to place the directory under the default document tree, such as /var/www/gbrowse2.

portdemo

The internet port on which the demo will run. The demo launches a new instance of Apache running under your user privileges. Because port 80 will usually already be taken by the system Apache, Build will choose an unused port like 8000 or 8080. You may manually select the port if you wish.

tmp

The directory in which GBrowse will store its working data, including users' session information (such as preferred tracks), uploaded data files, and temporary image files. The default is to place these files into /var/tmp/gbrowse2.

wwwuser

The account under which the system Apache runs, often "nobody", "www-data" or "httpd." If you do not know, you can find out by running ps aux | grep -i apache on a system that has Apache already running. The first column of the output contains the name of the user account.

Once you have configured GBrowse, the values you chose will stick until you run ./Build reconfig. You can also bypass interactive configuration by directly passing Build.PL one or more of the configuration options on the command line:

perl Build.PL --apachemodules=/usr/local/share/apache/libexec \
              --cgibin=/var/lib/cgi \
              --conf=/etc/gbrowse \
              --htdocs=/usr/local/docs/gbrowse \
              --databases=/usr/local/gbrowse/databases \
              --tmp=/tmp/gbrowse \
              --portdemo=9000 \
              --wwwuser=fred

The options passed on the command line will become the defaults for ./Build config will be used during installation, and will also become the defaults if you later run ./Build config or ./Build reconfig.

Running the GBrowse Demo (optional)

Before you install GBrowse, you may wish to run its demo. This will attempt to launch a correctly configured instance of Apache running under your own account. To launch the demo, run ./Build demo:

% ./Build demo
Demo is now running on http://localhost:8000
Run "./Build demostop" to stop it.

You can now point your web browser at http://localhost:8000 (or whatever the build message specifies), and interact with the GBrowse web site, browse sample genomes and otherwise test the waters. When you are done, run ./Build demostop to stop Apache and clean up.

Final Installation

To install GBrowse and its support files permanently, run ./Build install as the superuser. This will copy GBrowse's library and support files into the locations chosen during configuration. It will then configure Apache to run GBrowse by writing the appropriate configuration directives into Apache's configuration file. Finally, it will attempt to restart Apache. If all goes well, you will see a note telling you to load http://localhost/gbrowse2. This will take you to an autogenerated page that describes the install configurations you chose, points to an example database to run, and gives pointers to documentation, tutorials and other useful information.

Debugging and Customizing the Installation

If you are having trouble with the installation, see Common Problems with GBrowse2 Installation. If you wish install GBrowse in your home directory because you do not have superuser privileges or for any other reasons, see Installing GBrowse2 in your Home Directory.

Customizing GBrowse

GBrowse's options and controlled by two types of configuration file. GBrowse.conf contains site-specific options that apply to all data sources. One or more Data source-specific configuration files define the options needed to create a specific genome browser.

GBrowse.conf

When you installed GBrowse, it created an initial GBrowse.conf configuration file in the directory you specified at configure time. The default location of this directory is /etc/gbrowse2. This file contains two types of information:

1. Global configuration options to apply to all data sources that you want to make available to users.
2. A list of the data sources, including their names and their source-specific configuration files.

Here is the default GBrowse.conf:

# 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            = /etc/GBrowse2   # overridden by environment variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
db_base                = /var/www/gbrowse2/databases
tmp_base               = /var/tmp/gbrowse2
tmp_slave              = /var/tmp/gbrowse2/slave

# These paths are relative to the config base
plugin_path    = plugins
language_path  = languages
templates_path = templates
moby_path      = MobyServices

# Session settings
session driver = driver:file;serializer:default
session args   = Directory /var/tmp/gbrowse2/sessions

titles are balloons = 1

# Debug settings
debug                  = 0
debug_external         = 0
debug_plugins          = 0

# Performance settings
renderfarm             = 1
cache time             = 2h
slave_timeout          = 45
global_timeout         = 60
remember_source_time   = 3M
remember_settings_time = 1M

# Appearance (can be overridden in per datasource config files)
# the stylesheet is relative to url_base if not otherwise noted
balloon tips        = 1
titles are balloons = 1
stylesheet          = css/gbrowse.css
plugins             = FastaDumper RestrictionAnnotator SequenceDumper Submitter
overview grid       = 0
detail grid         = 1
overview bgcolor    = lightblue
detail bgcolor      = lightgoldenrodyellow
key bgcolor         = beige
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 />

# 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

# 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 = yeast

[yeast]how long 
description   = S. cerevisiae chromosomes I & II
path          = yeast_chr1+2.conf

[renderfarm]
description  = Renderfarm demo (gbrowse_slave must be running!)
path         = yeast_renderfarm.conf

GBrowse.conf consists of several sections. The [GENERAL] section is the largest, and describes options that apply to GBrowse globally. Below this are one or more source-specific sections with short descriptive names like [yeast]. Each of these short sections describes a genome datasource which you will make available for browsing. how long

The GBrowse.conf [GENERAL] Section

The [GENERAL] section defines a large number of options, most of which you will never need to change. The format of an option is the option name, an equals sign, and the value of the option. There may be whitespace before and after the equals sign. To continue long option values across multiple lines, begin the second and subsequent lines with one or more spaces or tabs; the additional whitespace will be treated as a single space. Lines beginning with the hash (#) symbol are comments.

Several options take true/false values. A false value is numeric 0. A true value is numeric 1, or indeed any other non-zero value (including the word true).

Paths and Directories

config_base, htdocs_base, url_base, db_base, tmp_base,tmp_slave

The first six options describe the location of GBrowse's configuration and support files. config_base is the location of GBrowse's datasource-specific configuration files, typically /etc/gbrowse2. htdocs_base specifies the location of GBrowse's static HTML files, stylesheets and javascript libraries. url_base is similar to htdocs_base and gives the location of same HTML files, stylesheets and javascript libraries in URL form. So, for example, if GBrowse's static files are located in /var/www/html/GBrowse and this maps in URL space to http://your.site/GBrowse, then htdocs_base will be /var/www/html/GBrowse and url_base will be /GBrowse. db_base describes the default location of in-memory databases. tmp_base points to the directory used for user sessions, uploads and other temporary files. Finally, tmp_slave describes the temporary directory used by GBrowse's optional rendering slaves (see Running a GBrowse2 Render Farm).

The config_base directive is overridden by the environment variable GBROWSE_CONF. This variable is set when Apache starts up, and can be found in /etc/apache2/conf.d/gbrowse2.conf, /etc/httpd/conf.d, or /etc/apache/conf.d, depending on how your system is layed out.

buttons,balloons,gbrowse_help,js

These four configuration options tell GBrowse where to find the images for its navigation buttons, popup balloons, help pages, and javascript libraries. Ordinarily you will not need to change these locations. The default locations are subdirectories of htdocs_base. If you specify a relative path, they will be taken as relative to htdocs_base (in filesystem space) and url_base (in URL space).

plugin_path, language_path, templates_path, moby_path

These configuration options specify where plugins, language translation files, templates and MOBY configuration files are located. If relative paths are given here, they are taken relative to the config_base. The default is to place them in subdirectories of config_base.

Session Settings

session driver, session args

These two options pass settings to the CGI::Session module, which is responsible for GBrowse's persistent user settings. As described in the CGI::Session documentation, session driver selects the driver to be used for storing and retrieving user session information, and session args passes additional arguments to the selected driver. The default is to use the standard "file" driver. To use the faster (but not universally available) DB_File driver, the options might look like this:

 session driver = driver:db_file;serializer:default
 session args   = FileName /var/tmp/gbrowse2/sessions.db

Debug Settings

The next set of options toggles on or off various debug flags, enabling you to watch what GBrowse2 is doing and help the developers catch and fix bugs. Their values are either 0 (no debugging messages) or 1 (activate debugging messages). When debugging is active, the messages will appear in the Apache error log, typically /var/log/apache2/error_log.

debug

This turns on messages about general GBrowse operations.

debug_external

This turns on messages concerning the uploading and processing of user-supplied tracks, as well as tracks fetched from remote sources via the DAS protocol.

debug_plugins

This turns on debugging messages concerning the operation of GBrowse's user-contributed plugins.

Performance Settings

This section contains a variety of performance-related settings that you may want to change in order to tune GBrowse for your needs.

renderfarm

This configuration directive turns on and off GBrowse's support for a rendering farm (see Running a GBrowse2 Render Farm). By default this support is enabled, but there no particular performance penalty if you choose not to take advantage of it. If you plan never to use the feature, set it to a false (zero) value:

 renderfarm = 0

cache_time

How long tracks will be cached before they are regenerated. This speeds up page load speed for frequently-accessed pages. The format is a number followed by a time unit, where units are s for second, m for minute, h for hour, d for day, and M for month. The default is "2h", or two hours.

slave_timeout

When running a GBrowse2 render farm, this option controls how long the master server will wait for one of its slaves before it times out and considers the slave "down". The units are seconds, 45 seconds by default.

global_timeout

If a database query, search or plugin takes longer than the number of seconds given by this option, GBrowse will time out and return an error to the user. The default is 60 seconds.

remember_source_time

This option controls how long the user's last-selected data source will be remembered in his or her session. The format is similar to cache_time and is a number followed by a time unit, where units are s for second, m for minute, h for hour, d for day, and M for month. The default is "3M" for three months.

remember_settings_time

This option controls how long the user's track configuration, which includes which tracks are turned on and their customized settings, will be remembered in his or her session. The format is the same as remember_source_time and is set to one month by default.

Appearance Settings

The following options control the appearance and behavior of GBrowse. Unlike the earlier options, any of them can be overridden on a per-datasource basis in datasource-specific configuration files simply by inserting the option into the [GENERAL] section of the datasource-specific config file.

balloon tips

This is a true/false option. If true, popup balloons are activated such that when the user mouses over a feature, additional information about that feature appears in a balloon.

titles are balloons

This is a true/false option. If true, popup balloons are automatically populated by default information about the feature unless a track has a balloon hover option that overrides the content. If false, then you will need to set the balloon hover option for the track in order for balloons to appear at all.

stylesheet

This option sets the path to the GBrowse cascading stylesheet (CSS) file. This sets such options as the page background color, font size, background image, and so forth. Edit this option here to change the appearance of all data sources, or add a stylesheet option to the [GENERAL] section of datasource-specific configuration files to change the appearance on a case-by-case basis.

plugins

This option selects which, if any, of the GBrowse plugins to offer to the user. It is a space-delimited list of plugin names. Plugins are Perl .pm modules that can be found in the plugins subdirectory of the GBrowse2 configuration directory. Select the ones you wish to activate, and put their in this configuration directive, minus the ".pm" extension. See GBrowse2 Plugins for a description of what each plugin does.

overview grid, regionview grid, detail grid

These two

too many landmarks

This option controls the maximum number of results to return when the user performs a wildcard search on the database. The default is 100.

The [GENERAL] Section

The [GENERAL] section consists of a series of name=value options. For example, the beginning of the yeast.conf sample configuration file looks like this:

[GENERAL]
description = S. cerevisiae (via SGD Nov 2001)
db_adaptor  = Bio::DB::GFF
db_args     = -adaptor dbi::mysql
              -dsn     dbi:mysql:database=yeast;host=localhost
aggregators = transcript alignment
user        =
passwd      =

Each option is a single word or phrase, usually in lower case. This is followed by an equals sign and the value of the option. You can add whitespace around the equals sign in order to increase readability. If a value is very long, you can continue it on additional lines provided that you put a tab or other whitespace on the continuation lines. For example:

description = S. cerevisiae annotations via SGD Nov 2001, and
            converted using the process_sgd.pl script

Any lines that begin with a pound sign (#) are considered comments and ignored.

During this discussion, you might want to follow along with one of the example configuration files.

The following [GENERAL] options are recognized:

• description

The description of the database. This will appear in the popup menu that allows users to select the data source and in the header of the page. Don't make it as long as the previous example! (You will want to change this.)

• db_adaptor

Tells GBrowse what database adaptor to use. By using different adaptors you can attach gbrowse to a variety of different databases. Currently the only stable adaptor you can use is Bio::DB::GFF, which is a standard set of adaptors contained in Bioperl.

• db_args

Arguments to pass to the adaptor for it to use when making a database connection. The exact format will depend on the adaptor you're using. For Bio::DB::GFF running on top of a MySQL database use a db_args like the following:

   db_args = -adaptor dbi::mysql
             -dsn     dbi:mysql:database=<db_name>;host=<db_host>

replacing <db_name> and <db_host> with the database and database host of your choice. For MySQL databases running on the localhost, you can shorten this to just "db_name".

If the database requires you to log in with a user name and password, use the following db_adaptor:

   db_args = -adaptor dbi::mysql
             -dsn     dbi:mysql:database=<db_name>;host=<db_host>
             -user    <username>
             -pass    <password>

replacing <username> and <password> with the appropriate values. In the example configuration files, we use a username of "nobody" and an empty password. This is appropriate if the database is configured to allow "nobody" to log in from the local machine without using a password.

To use the Oracle version of Bio::DB::GFF, use these arguments:

   db_args = -adaptor dbi::oracle
             -dsn dbi:oracle:database=db_service

Where db_description should be replaced with the name of the desired database service definition. See the documentation for the Perl dbd::Oracle database driver for more information about the -dsn format.

To use the in-memory version of Bio::DB::GFF, use these arguments:

 db_args = -adaptor memory
           -dir   /path/to/directory

The indicated directory should contain one or more GFF and FASTA files, distinguished by the filename extensions .gff and .fa respectively.

• allow remote callbacks

This option, if true, allows users to place callbacks ("sub ....") in the configuration sections of uploaded files.The callbacks will be executed in a Safe::World compartment, which forbids access to the file system, dangerous operations such as "exec" and "eval", and access to anything but the Bio::Graphics::SeqFeature and Bio::Graphics::Glyph classes. The option also affects remote annotation tracks. For this option to work, the Safe::World module must be installed from CPAN.

• aggregators

This option is only valid when used with Bio::DB::GFF adaptors, and lists one or more aggregators to use for complex features. It is possible to declare your own aggregator here using a special syntax described in "B7. Declaring New Aggregators."

To disable the default aggregators, leave this setting blank, as in:

    aggregators=

To activate the default aggregators of "transcript," "clone," and "alignment," comment this setting out entirely:

   # aggregators =

Do not use aggregators with Bio::DB::SeqFeature::Store, BioSQL, or Chado.

• user

The user name for the gbrowse script to log in under if you are not using "nobody". This is exactly the same as providing the -user option to db_args, and is deprecated.

• pass

The password to use if the database is password protected. This is the same as providing the -pass option to db_args, and is deprecated.

• gbrowse root

This specifies the URL of GBrowse's static files on your server, such as stylesheets, images and JavaScript files. The default is /gbrowse.

• stylesheet

Location of the stylesheet used to create the GBrowse look and feel. You can give a relative address (e.g. "gbrowse.css"), in which case GBrowse will look relative to the URL specified by "gbrowse root." Alternatively, you can specify an absolute URL (e.g. "/stylesheets/mysite.css").

• buttons

URL in which the various graphical buttons used by GBrowse are located. The relative and absolute addressing rules described for "stylesheet" apply here as well. (You will probably not need to change this.)

• js

URL in which the gbrowse javascript helper function files are located. The relative and absolute addressing rules described for "stylesheet" apply here as well. (You will probably not need to change this).

• tmpimages

URL of a writable directory in which GBrowse can write its temporary images. The format is:

 tmpimages = <tmpimages_url> <tmpimages_path>

Where <tmpimages_url> is the directory as it appears as a URL and <tmpimages_path> is the physical path to the directory as it appears to the filesystem. Usually the physical path is just the URL with the DocumentRoot configuration variable prepended to it, in which case only the URL is needed. However, if the URL is defined using an Alias directive, then the path argument is mandatory.

The tmpimages option is mandatory.

The relative and absolute addressing rules described for "stylesheet" apply here as well.

NOTE: The path argument is ignored if gbrowse is running under modperl, because modperl allows the URL to be translated into a physical directory programatically.

• plugins

This is a list of plugins that you want to be available from gbrowse. Plugins are a way for third-party developers to add functionality to gbrowse without changing its core source code. Plugins are stored on the gbrowse configuration directory under a subdirectory named "plugins."

A good standard list of plugins is:

   plugins = SequenceDumper FastaDumper RestrictionAnnotator

See the contents of conf/plugins and contrib/plugins for more plugins that you can install.

• quicklink plugins

This is a list of plugins that you want to appear as links in the link bar (which includes the [Bookmark this] and [Link to Image] links). Selecting one of these links is equivalent to choosing the plugin from the popup menu and pressing the "Go" button. The popup will continue to appear in the popup menu.

• plugin_path

By default gbrowse searches for plugins in its standard location of conf/plugins. You can store plugins in a non-standard location by providing this option with a space-delimited list of additional directories to search in.

• galaxy outgoing

If you would like GBrowse to be able to send data to the Galaxy bioinformatics analysis tool, then set this option to the URL for the Galaxy server you would like to use. A good default is:

  galaxy outgoing = http://main.g2.bx.psu.edu/

Without this option, GBrowse will be able to receive and process queries from Galaxy servers, but will not be able to initiate a connection. (Note, this option used to be named "galaxy", which still works for backward compatibility)

• galaxy incoming

Use this option to change the URL that Galaxy will use when it tries to fetch GFF3-formatted data from GBrowse. The default is:

  http://yourhostname/cgi-bin/gbgff

However, the default will break if the Gbrowse web server is behind a web proxy that uses a different hostname. In this case, you will need to set the location of the gbgff script explicitly.

• galaxy build name

To be most effective, Galaxy needs to know the genome build name corresponding to the annotations contained in the current database so that it can integrate GBrowse-generated data with other data sets. Each species has its own build name conventions, for example "hg18" for UCSC build number 18. Set this to the build name of your choice. If not present, the value default to the database name.

• hilite fill, hilite outline

These options control the color of the selection rectangles that appear in the overview and regionview when you are zoomed into a region. The hilite fill controls the color of the rectangle interior, and the hilite outline controls the color of the rectangle outline. Colors can be specified by name (e.g. "pink"), or in HTML #RRGGBB format.

• image widths

The image widths option controls the set of image sizes to offer the user. Its value is a space-delimited list of pixel widths. The default is probably fine. Note that the height of the image depends on the number of tracks and features, and cannot be controlled.

• default width

The default width is the image width to start off with when the user invokes the browser for the first time. The default is 800.

• default features

The default features option is a space-delimited list of tracks to turn on by default. You will probably need to change this. For example:

    default features = Genes ORFs tRNAs Centromeres:overview

The syntax for annotation plugins is slightly different. To activate an annotation plugin track by default, preface the plugin's name with "plugin:"

    default features = Genes ORFs Centromeres:overview
                       plugin:RestrictionAnnotator

• reference class

gbrowse needs to know the class of the reference sequences that other features are placed on. The default is Sequence. If you want to use another class, such as Contig, please indicate the class here (if you don't, certain features such as the keyword search will fail):

     reference class = contig

• initial landmark

This option controls what feature to show when the user first visits a gbrowse database and has not yet performed a search. If not present, gbrowse displays a page with the search area and options, but no overview or panel.

Example:

      initial landmark = Chr1

• drag and drop

If this is set to true, then code will be activated that lets the user pick up and drag individual tracks in order to change their vertical stacking order. For this to work, the user must have a relatively recent browser (IE 5 or higher, Firefox 1.5 or higher) and must have JavaScript activated.

It is off by default for compatibility with older browsers.

• disable wildcards

Ordinarily a user can type in "YAL*" to find all features with names beginning with "YAL". This option, if set to a true value, disables wildcard searching.

• truecolor

If this option is present and true, then GBrowse will create 24-bit (truecolor) images. This is mainly useful when using the "image" glyph, which allows you to paste arbitrary images onto the genome map. Do not use this option unless you need it, because it slows down drawing and makes the images much larger.

• units, unit_divider

The units option allows GBrowse to display units on an alternate scale (for example, (centi)Morgans), and the unit_divider provides the converstion factor between base pair units (which is what must be specified in the GFF file) and the specified units. For example if it is known that 5010 base pairs is equal to one Morgan, 5010 would be specified for the unit_divider. Note that if unit_divider is specified, max segment, default segment and and zoom levels will all be interpreted in terms of the specified units.

• max segment, min segment

These options control the size of segments that will be shown in the detailed view.

The max segment option sets an upper bound on the maximum size segment that will be displayed on the detailed view. Its value is in the selected units. Above this limit, the user will be prompted to select a smaller region on the birds-eye view. The default is 1,000,000 base pairs.

If the user tries to view a segment smaller than the min segment option, then the segment will be resized to be this size. The default is 20 bp.

• default segment

The default segment option sets the width of the segment (bp) that will be displayed when the user clicks on the birds-eye view without previously having set a desired magnification. You may want to adjust this value.

• zoom levels

GBrowse allows unlimited zoom levels. This option selects the width of each level, in bp. For example:

     zoom levels = 1000 2000 5000 10000 20000 40000 100000 200000

• region segment

If this configuration option is set, a new "region panel" will appear that is intermediate in size between the overview and the detail panel. The value of this option becomes the size of the region panel in base pairs.

• region sizes

This contains a space-delimited list of region panel sizes to present to the user in a popup menu:

    region sizes   = 5000 10000 20000

• show sources

A 0 (false) or 1 (true) value which controls whether or not to show the popup menu displaying the defined data sources. Set this to 0 if you wish for the names of the data sources to be hidden. If not present, this option defaults to 1 (true).

Note that all data sources will need to have this option defined in order for it to take effect across all databases.

• default varying

The track selection table will be sorted alphabetically, by default; setting this variable to true will cause the tracks to appear in the same order as they appear in the configuration file.

• keyword search max

By default, gbrowse will limit the number of keyword search results to 1,000. The order in which the 1,000 hits are returned depends on how the database was loaded, and so you may see odd patterns, such as only hits on a particular chromosome being displayed. To raise the limit on keyword search results, set "keyword search max" to the desired maximum value.

• overview units

This option controls the units that will be used on the scale for the birds-eye view display. Possible values are "bp" (base pairs), "k" (kilobases), "M" (megabases), and "G" (gigabases). If this option is omitted, the browser will guess the most appropriate unit.

• overview bgcolor

This is the color for the background of the birds-eye view.

• cache time

The server will cache track images for a period of time in order to speed up performance. After the time has expired, the cached version of the image will not be used. This option specifies the time, in hours, that images will be cached. The default is 1 hour.

If you are debugging your config file and want to see uncached images, call gbrowse with the CGI option nocache=1.

• version

An optional numeric version for this configuration file. Every time gbrowse runs a user's request, it checks the value of the config file version against a version number saved in the user's settings. Of the current version is higher than the saved version, then gbrowse will reset the user's page session to its default values. Use this if you want to reset all users sessions to a known working state, or to draw their attention to a new feature you've added.

Example:

  version = 1.1

• detailed bgcolor

This is the color for the background of the detailed view.

• request timeout

This is the timeout value for requests. If a user requests a large region and the request takes more than the indicated number of seconds, then the request will timeout and the user will be advised to choose a smaller region. The default is 60 seconds (one minute). You can make the timeout longer or shorter than this.

• head

This is content to insert into the HTML <head></head> section. It is the appropriate place to stick JavaScript code, etc. It can be a code reference if you wish.

• header

This is a header to print at the top of the browser page. It is any valid HTML, and can span multiple lines provided that the continuation lines begin with white space.

It is also possible to place an anonymous Perl subroutine here. The code will be invoked during preparation of the page and must return a string value to use as the header. See COMPUTED OPTIONS for details.

Example:

   header = <h1>Welcome to the Volvox Sequence Page</h1>

• onload

This is the name of javascript function(s) to be called via the page body's onload event handler. Any text included here will be used to mark-up the <body> element of the html printed by the gbrowse script. The onload event handler will fire *after* the page is finished loading, so this setting will be useful for running javascript functions that rely on all or part of the HTML having been loaded and interpreted by the browser. The onload text must use correct javascript syntax. For example:

 onload = alert('I am about to do something');doSomething('arg1','arg2')

will result in

<body onload="alert('I am about to do something');doSomething('arg1','arg2')">

• footer

This is a footer to print at the bottom of the browser page. It is any valid HTML, and can span multiple lines provided that the continuation lines begin with white space.

It is also possible to place an anonymous Perl subroutine here. The code will be invoked during preparation of the page and must return a string value to use as the header. See COMPUTED OPTIONS for details.

Example:

       For the source code for this browser, see the <a href="http://www.gmod.org">
       Generic Model Organism Database Project.</a>  For other questions, send
       mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.

• examples

You can provide GBrowse with some canned examples of "interesting regions" for the user to click on. The examples option, if present, provides a space-delimited list of interesting regions. For example:

      examples = II  NPY1 NAB2 Orf:YGL123W

• automatic classes

When the user types in a search string that is not qualified by a class (as in EST:yk1234.5), GBrowse will automatically search for a matching feature of class "Sequence". You can have it search for the name in other classes as well by defining the "automatic classes" option.

Example:

       automatic classes = Symbol Gene Clone

When the user types in "hb3", the browser will search first for a Sequence feature of class hb3, followed in turn by matching features in Symbol, Gene and Clone. The search stops when the first match is found. Otherwise, the browser will proceed to a full text search of all the comment fields.

• search attributes (Bio::DB::SeqFeature::Store adaptor only)

When the browser has searched the name and alias of features without success, it will do a whole database keyword search by calling the database's search_notes() method. By default this will search the text of all attributes, including such things as protein sequence. The Bio::DB::SeqFeature::Store database is a bit smarter about searching, and will only, by default, search attributes named "Note". You can expand the search by giving a list of attribute names to the "search attributes" option.

• remote sources

This option allows you to add remote annotation sources to the menu of such sources at the bottom of the main window. The format is:

     remote sources = "Menu Label 1" http://url1.host.com/etc/etc
                      "Menu Label 2" http://url2.host.com/etc/etc

• instructions, search_instructions, navigation_instructions

You may override the default instructions (as defined in the language-specific configuration files in conf/lang) by setting these options. For example:

        instructions = "Type in the name of a contig or clone."

• no search

If you don't want the "Landmark or Region" textbox to appear, set this to true. The user will still be able to search the database by appending q=<search term> to the URL.

         no search = 1

• no autosearch

If this option is set to a true value, then the user's previous search will not be automatically re-executed the next time he visits gbrowse. Instead, the previous search will be pasted into the "Landmark or Region" box and the user will have to press "Search" to reexecute it.

• category tables

This option allows you to group the on/off checkboxes for set of tracks into a rectangular M x N table. It can be used to highlight the experimental design of a microarray or ChIP-on-Chip experiment.

The format is:

category tables = 'category name' 'columnlabel1 columnlabel2 columnlabel3' 'rowlabel1 rowlabel2 rowlabel3'

Where "category name" is the name of the track category (described in more detail below), "columnlabelN" is the label of the Nth column, and "rowlabelN" is the label of the Nth row. For example:

category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'

This will set up all the tracks labeled with category "ArrayExpts" so that they are displayed in a 2x3 table like this:

                temperature     anaerobic      aerobic
  strain-A      track 1          track 4       track 7
  strain-B      track 2          track 5       track 8
  strain-C      track 3          track 6       track 9

"track N" will be replaced with the name you selected for the track.

Additional category tables can be specified using continuation lines:

category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'
                  'CHiP-Chip'  'TFX1 ONE-CUT PHA4' '16-cell-stage 320-cell-stage adult'

See the tutorial for more details.

• instructions section =item * search section =item * overview section =item * region section =item * details section =item * tracks section =item * display_settings section =item * upload_tracks section

These options control which sections are displayed and whether they are initially open or collapsed. Their values are one of:

open     Show the section initially open
closed   Show the section initially collapsed
off      Do not show the section at all

For example "instructions section = closed" will initially show the instructions section in collapsed form when the user visits gbrowse for the first time. "upload_tracks section = off" will disable the uploads section entirely.

Note that turning off the details section will effectively disable gbrowse, but you might want to do this if you want to show the overview section only. Turning off the search section will also disable the navigation buttons. If you want to disable searching selectively, you should use the "no search" option instead.

• html1, html2, html3, html4, html5, html6

These options allow you to insert HTML into the GBrowse page at strategic places. Eventually this will be replaced with an HTML template system, but for now, this is the best we have.

These can be code references. One useful thing to do is to use the language translator to insert language-specific HTML. Here's an example provided by Marc Logghe:

   html2 = sub {
       my $go = $main::CONFIG->tr('Go');
       return
       qq(

       Dump:<input type="button" value="Assembly" onclick="window.open('gbrowse?plugin=AssemblyDumper;plugin_action=$go');">
       <input type="button" value="Reads" onclick="window.open('gbrowse?plugin=ReadDumper;plugin_action=$go');">

       );
      }

If you use a coderef for the html options, the subroutine is passed two arguments. The first argument is a Bio::Das::SegmentI object (see the manual page for Bio::DB::GFF::RelSegment for details). The second argument is a hashref containing the user's settings for the current page.

• keystyle, empty_tracks

These two general options control the appearance of the keys printed on the detailed view. keystyle takes one of two values "between" or "beneath".

      keystyle = between
      Print the track labels between the tracks themselves.

      keystyle = beneath
      Print the track labels at the bottom of the detailed view.

The "empty_tracks" option controls what to do when a track has no features in it. Possible values are:

      empty_tracks = key
      Print just the key (the track label).

      empty_tracks = suppress
      Suppress the track completely.

      empty_tracks = line
      Draw a solid line across the track.

      empty_tracks = dashed
      Draw a dashed line across the track.

The default value is "key."

• background, postgrid

These two options can be used to place custom background images in the details panel and are useful for advanced operations such as colorizing the panel to show gaps in the assembly. Either option accepts either the path to a graphics file to be tiled onto the background, or a callback subroutine. In the case of the latter the callback will passed a two argument list consisting of the GD::Image object and the Bio::Graphics::Panel object. This gives the callback a chance to draw on top of the background using GD library calls.

The only difference between the two options is the time that they are applied relative to the grid that shows base pair coordinates. The background option is invoked before the grid is drawn so that the grid appears on top of it. The postgrid option is invoked after the grid is drawn, so that anything the option draws appears on top of the grid. See http://sourceforge.net/mailarchive/message.php?msg_id=12116755 for an example of using this feature to show assembly gaps as vertical gray regions.

For a clever example of how to use postgrid calls, see the SynView synteny browser in the contrib directory of the GBrowse distribution. It uses a standard GBrowse configuration file with postgrid calls to draw trapezoids between glyphs to show synteny. For an example of how this looks, see http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/?start=101357;stop=121356;ref=MAL12;width=800;version=100;label=AnnotatedGenes-SyntenySpansVivaxMC-SyntenyGenesVivaxMC.

• image_padding = 25
• pad_left = 50
• pad_right = 30

The image_padding option will add the indicated amount of whitespace (in pixels) to the right and left of the detail panel. The default is 25 pixels. You may need to adjust this if you are using the xyplot glyph and finding that the scale (which is printed outside the graph area) is being cut off.

You can individually adjust the left and right padding using pad_left and pad_right, which, if present, will supersede image_padding.

• show track categories

If this option is set to a true value, then tracks that have been assigned to categories (using the "category" option described later), will have their categories included in their labels. For example, a track of key "Protein matches" and category "vertebrate" will be displayed in a track labeled "Protein match (vertebrate)".

The default is false.

• das mapmaster

This option, which should appear somewhere in the [GENERAL] section, indicates that the database should be made available as a DAS source. The value of the option corresponds to the URL of the DAS reference server for this data source, or "SELF" if this database is its own reference server. (See http://www.biodas.org/ for an explanation of what reference servers are.)

Please see DAS_HOWTO for more information on using DAS with GBrowse.

• proxy, http proxy, ftp proxy

If your web server is behind a firewall and needs to use a proxy in order to access remote HTTP or FTP sites, then one or more of these options needs to be specified in order for the "add remote annotations" feature to work (both for file-based and DAS-based remote annotations). "http proxy" will set the proxy to use for outgoing HTTP connections, "ftp proxy" will set the proxy to use for outgoing FTP connections, and "proxy" will set both. The value is the URL of the proxy:

  proxy = http://myproxy.myorg.com:9000

• session driver
• session args

These options fine-tune how gbrowse manages its state-maintaining sessions. GBrowse uses CGI::Session to store session data on the server. By default (if neither of these options is present), it uses CGI::Session's "file" driver and "default" serializer. The session files are stored in the "sessions" directory underneath the directory specified by the "tmpimages" option (e.g. /usr/local/apache/htdocs/gbrowse/tmpimages/sessions).

The "session driver" option will be passed to CGI::Session->new() as the first argument. It specifies the driver, serializer and ID generator according to the syntax described in the CGI::Session manual page. The "session args" option will be passed to CGI::Session->new() as the third argument. It specifies additional parameters to be passed to the selected driver.

For example, here is how to create session data that is stored in the MySQL "test" database under a table named "gbrowse_sessions." The session data will be stored in binary form by the Storable module:

session driver = driver:mysql;serializer:storable
session args   = DataSource test
                 TableName  gbrowse_sessions

See the CGI::Session documentation for information about setting up the MySQL table and appropriate permissions.

You might also want to read about CGI::Session::ID::salted_md5 for an ID generation algorithm that should be more secure (but slightly slower) than the default one.

You will not ordinarily need to use these settings, as the defaults seem to work well. If you change these defaults, be sure to change them in all configuration files; otherwise weird stuff will happen when moving from one data source to another.

• remember settings time

The length of time to remember page-specific settings in the format "+NNNu", where NNN is a number and "u" is a unit ("w" = weeks, "d" = days, "M" = months). For example:

 remember settings time = +3M   # remember settings for 3 months

The users' settings, which includes uploaded files, track options and plugin configuration, will be reset to the default if he or she fails to visit the site within the time specified.

The default value is 1 month.

See the CGI manual page for more information on the time format.

• remember cookie time

This is the length of time before the user's session cookie will stay on disk before it expires. It should be significantly longer than "remember settings time." The default is 12 months.

• remember source time

Deprecated. Use "remember cookie time" instead.

• msie hack

GBrowse uses HTTP POST to transfer the current page settings to the web server. Because of the way that Microsoft Internet Explorer caches pages, when users of this browser press the "Back" button, MSIE will display an annoying alert that prompts the user to reload the page.

When you set "msie hack" to a true value, Gbrowse will use the GET request when it detects MSIE in use. This will fix the "Back" button issue, but will put very long URLs in the Location box. It is your choice which of these is more annoying to your users.

• suppress_menu

This option will cause the browser to ignore your configuration file when building the source menu. Your sourcse will still be accessible by URL using the gbrowse/yourSource or gbrowse?src=yourSource syntax. One possible application for this feature would be to your data source while you are testing a new configuration.

The [TRACK DEFAULTS] section

The track defaults section specifies default values for each track. The following common options are recognized:

            glyph
            height
            bgcolor
            fgcolor
            fontcolor
            font2color
            strand_arrow

These options control the default graphical settings for any annotation types that are not explicitly specified. See the section below on controlling the settings. Any of the options allowed in the [track] sections described below are allowed here.

• label density

When there are too many annotations on the screen GBrowse automatically disables the printing of identifying labels next to the feature. "label density" controls where the cutoff occurs. The value in the example files is 25, meaning that labels will be turned off when there are more than 25 annotations of a particular type on display at once.

• bump density

When there are too many annotations on the screen GBrowse automatically disables collision control. The "bump density" option controls where the cutoff occurs. The value in the example files is 100, meaning that when there more than 100 annotations of the same type on the display, the browser will stop shifting them verticially to prevent them from colliding, but will instead allow them to overlap.

• link

The link option creates a default rule for creating outgoing links from the GBrowse display. When the user clicks on a feature of interest, he will be taken to the corresponding URL.

The link option's value should be a URL containing one or more variables. Variables begin with a dollar sign ($), and are replaced at run time with the information relating to the selected annotation. Recognized variables include:

    $name        The feature's name (group name)
    $id          The feature's id (eg, PK from a database)
    $class       The feature's class (group class)
    $method      The feature's method
    $source      The feature's source
    $ref         The name of the sequence segment (chromosome, contig)
                    on which this feature is located
    $description The feature's description (notes)
    $start       The start position of this feature, relative to $ref
    $end         The end position of this feature, relative to $ref
    $segstart    The left end of $ref displayed in the detailed view
    $segend      The right end of $ref displayed in the detailed view

For example, the wormbase.conf file uses this link rule:

    link = http://www.wormbase.org/db/get?name=$name;class=$class

At run time, if the user clicks on an EST named yk1234.5, this will generate the URL

    http://www.wormbase.org/db/get?name=yk1234.5;class=EST

It is possible to override the global link rule on a feature-by-feature basis. See the next section for details on this. It is also possible to declare a subroutine to compute the proper URL dynamically. See COMPUTED OPTIONS for details.

A special link type of AUTO will cause the feature to link to the gbrowse_details script, which summarizes information about the feature. The default is not to link at all.

• link_target

By default links will replace the contents of the current window. If you wish, you can specify a new window to pop up when the user clicks on a feature, or designate a named window or frame to receive the contents of the link. To do this, add the "link_target" option to the [TRACK DEFAULTS] section or to a track stanza. The format is this:

      link_target = _blank

The value uses the HTML targetting rules to name/create the window to receive the value of the link. The first time the link is accessed, a window with the specified name is created. The next time the user clicks on a link with the same target, that window will receive the content of the link if it is still present, or it will be created again if it has been closed. A target named "_blank" is special and will always create a new window.

The "link_target" option can also be computed dynamically. See COMPUTED OPTIONS for details.

• title

The title option controls the "tooltips" text that pops up when the mouse hovers over a glyph in certain browsers. The rules for generating titles are the same as the "link" option discussed above.The "title" option can also be computed dynamically. See COMPUTED OPTIONS for details.

Note HTML characters such as "<", ">" and "&" are not automatically escaped from the title. This lets you do neat stuff, such as create popup menus, but also means that you need to be careful. In particular, you must not use the quote character (") in the title, but either use the " entity, or the single quote ('). The function CGI::escapeHTML() is available to properly escape HTML characters in dynamically-generated titles.

The special value "AUTO" causes a default description to appear describing the name, type and position of the feature. This is also assumed if the title option is missing or blank.

See CONFIGURE BALLOON TOOLTIPS for the ability to created rich tooltips including images and links.

• landmark_padding = 1000

The landmark_padding option will add the indicated number of base pairs to the right and left of all landmarks that are searched for by name.

Track Sections

Any other [Section] in the configuration file is treated as a declaration of a track. The order of track sections will become the default order of tracks on the display (the user can change this later). Here is a typical track declaration from yeast.conf:

[Genes]
feature      = gene:sgd
glyph        = generic
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height       = 6
description  = 1
key          = Named gene

This track is named "Genes". You may use a short mnemonic if you prefer; this will make the URL shorter when the user bookmarks a view he or she likes. Track names can contain almost any character, including whitespace, but cannot contain the "-" or "+" signs because these are used to separate track names in the URL when bookmarking. [My Genes] is OK, but [My-Genes] is not.

As in the general configuration section, the track declaration contains multiple name=value option pairs.

Valid options are as follows:

feature

This relates the track to one or more feature types as they appear in the database. Recall that each feature has a method and source. This is represented in the form method:source. So, for example, a feature of type "gene:sgd" has the method "gene" and the source "sgd".

It is possible to omit the source. A feature of type "gene" will include all features whose methods are "gene", regardless of the source field. It is not possible to omit the method. It is possible to have several feature types displayed on a single track. Simply provide the feature option with a space-delimited list of the features you want to include. For example:

   feature = gene:sgd stRNA:sgd

This will include features of type "gene:sgd" and "stRNA:sgd" in the same track and display them in a similar fashion.

remote feature

This relates the track to a remote feature track somewhere on the Internet. The value is a http: or ftp: URL, and may correspond to a static file of features in GFF format, gbrowse upload format, a CGI script, or a DAS source. When this option is active, the "feature" option and most of the glyph control options described below are ignored, but the "citation" and "key" options are honored.

Example:

remote feature = http://www.wormbase.org/cgi-bin/das/wormbase?type=mRNA

glyph

This controls the glyph (graphical icon) that is used to represent the feature. The list of glyphs and glyph-specific options are listed in the section GLYPHS AND GLYPH OPTIONS. The "generic" glyph is the default.

bgcolor

This controls the background color of the glyph. The format of colors is explained in GLYPHS AND GLYPH OPTIONS.

fgcolor

This controls the foreground color (outline color) of the glyph. The format of colors is explained in GLYPHS AND GLYPH OPTIONS.

fontcolor

This controls the color of the primary font of text drawn in the glyph. This is the font used for the features labels drawn at the top of the glyph.

font2color

This controls the color of the secondary font of text drawn in the glyph. This is the font used for the longish feature descriptions drawn at the bottom of the glyphs.

height

This option sets the height of the glyph. It is expressed in pixels.

strand_arrow

This is a true or false value, where true is 1 and false is 0. If this option is set to true, then the glyph will indicate the strandedness of the feature, usually by drawing an arrow of some sort. Some glyphs are inherently stranded, or inherently non-stranded and simply ignore this option.

label

This is a true or false value, where true is 1 and false is 0. If the option is set to true, then the name of the feature (i.e. its group name) is printed above the feature, space allowing.

description

This is a true or false value, where true is 1 and false is 0. If the option is set to true, then the description of the feature (any Note fields) is printed below the feature, space allowing.

key

This option controls the descriptive key that is drawn in the key area at the bottom of the image. It also appears in the checkboxes that the end user uses to switch tracks on and off. If not specified, it defaults to the track name.

citation

If present, this option creates a human-readable descriptive paragraph describing the feature and how it was derived. This is the text information that is displayed when the user clicks on the track name in the checkbox group. The value can either be a URL, in which case clicking on the track name invokes the corresponding URL, or a text paragraph, in which case clicking on the track name generates a page containing the text description. Long paragraphs can be continued across multiple lines, provided that continuation lines begin with whitespace.

link, title, link_target

These options are identical to the similarly-named options in the [GENERAL] section, but change the rules on a track-by-track basis. They can be used to override the global rules. To force a track not to contain any links, use a blank value.

box_subparts

If this option is greater than zero, then gbrowse will generate imagemap rectangles for each of the subparts of a feature (e.g. the exons within a transcript), allowing you to link each subpart separately. The numeric value will control the number of levels of subfeatures that the boxes will descend into. For example, if using the "gene" glyph, set -box_subparts to 2 to create boxes for the whole gene (level 0), the mRNAs (level 1) and the exons (level 2).

feature_low

If this option is present, GBrowse will use the list of feature types listed here at resolution views. (This is one of the ways that semantic zooming is implemented.) This allows you, for example, to switch off detailed exon, UTR, promoters and other within-the-gene features, and just show the start and stop of the transcription unit.

global feature

If this option is present and set to a true value (e.g. "1"), GBrowse will automatically generate a pseudo-feature that starts at the beginning of the currently displayed region and extends to the end. This is often used in conjunction with the "translation" and "dna" glyphs in order to display global characteristics of the sequence. If this option is set, then you do not need to specify a "feature" option.

group_pattern

This option lets you connect related features by dotted lines based on a pattern match in the features' names. A typical example is connecting the 5' and 3' read pairs from ESTs or plasmids. See GROUPING FEATURES for details.

group_on

For Bio::DB::SeqFeature::Store databases only, the group_on field allows you to group features together by display_name, target or any other method. This is mostly useful for XY-plot data, where you may want to dynamically group related data points together so that they share the same vertical scaling.

Example:

       group_on = display_name

(this feature is under refinement and may change in the future)

restrict

This option allows you to restrict who is allowed to view the current track by host name, IP address or username/password. See AUTHENTICATION AND AUTHORIZATION for details.

category

This option allows you to group tracks into different groups on the GBrowse display in addition to the default group called 'General'. For example, if you wanted several tracks to be in a separate group called "Genes", you would add this to each of the track definitions:

 category = Genes

As of GBrowse version 1.7, it is possible to create subcategories using this syntax:

 [label1]
 category = Genes:Coding
 ...

 [label2]
 category = Genes:Non-coding

This will create a section in the tracks panel called "Genes", which will have two subsections called "Coding" and "Non-coding". The track named "label1" will be placed in the first section, while the track named "label2" will be placed in the second.

Subcategories can be nested arbitrarily.

If all tracks are categorized, then the "General" category will not be displayed. If you have used a "category tables" option in the [GENERAL] section of the configuration file, then the names of the tracks labeled with this category will be placed into a table of the appropriate dimensions. Tracks will be placed into the table in column-major format: you should first list stanzas for all rows of column 1, then all rows of column 2, etc.

See the tutorial for more details.

das category, das landmark, das flatten, das subparts, das superparts, das glyph, das type

All these options pertain to exporting the GBrowse database as a DAS data source. Please see DAS_HOWTO for more information.

A large number of glyph-specific options are also recognized. These are described in the next section.

Glyphs and Glyph Options

A large variety of glyphs are available, and more are being added as the Bio::Graphics module grows.

A list of the common glyphs and their options is provided by the GBrowse itself. Click on the "[Help]" link in the section labeled "Upload your own annotations". This page also lists the valid foreground and background colors. Most of the glyphs are found in the BioPerl distribution, but a few are distributed directly with GBrowse.

The most popular glyph types are:

 Glyph                 Description
 -----                 -----------

 generic               a rectangle
 allele_tower          allele found at a SNP position
 arrow                 an arrow
 anchored_arrow        a span with vertical bases |-----|.  If one
                       or the other end of the feature is off-screen, the
                       base will be replaced by an arrow.
 box                   another rectangle; doesn't show subparts of features
 cds                   shows the reading frame of spliced transcripts; used
                       in conjunction with the "coding" aggregator.
 diamond               a point-like feature represented as a triangle
 dna                   DNA and GC content
 heterogeneous_segments a multi-segmented feature in which each segment can
                       have a distinctive color.  For Jim Kent's WABA features,
                       this works with the waba_alignment aggregator.
 idiogram              this takes specially-formatted feature data and turns it
                       into an idiogram of a Giemsa-stained metaphase chromosome
 image                 this embeds photographic images and/or diagrams on features
 processed_transcript  multi-purpose representation of a spliced mRNA, including
                       positions of UTRs
 segments              a multi-segmented feature such as an alignment
 span                  like anchored_arrow, except that the ends are
                       truncated at the edge of the panel, not turned
                       into an arrow
 trace                 reads an SCF trace file and draws a graphic representation
 triangle              a point-like feature represented as a diamond
 transcript            a gene model
 transcript2           a slightly different representation of a gene model
 translation           1-, 3- and 6-frame translations
 wormbase_transcript   yet another gene model that can show UTR segments
                       (for features that conform to the WormBase gene
                       schema). Used in conjunction with the
                       "wormbase_gene" aggregator.
 xyplot                histograms and line plots

A more definitive list of glyph options can be found in the Bio::Graphics manual pages. Consult the manual pages for the following modules:

 Glyph                         Manual Page
 -----                         -----------

 (common options for all)      Bio::Graphics::Glyph
 allele_tower                  Bio::Graphics::Glyph::allele_tower
 arrow                         Bio::Graphics::Glyph::arrow
 anchored_arrow                Bio::Graphics::Glyph::anchored_arrow
 box                           Bio::Graphics::Glyph::box
 cds                           Bio::Graphics::Glyph::cds
 crossbox                      Bio::Graphics::Glyph::crossbox
 diamond                       Bio::Graphics::Glyph::diamond
 dna                           Bio::Graphics::Glyph::dna
 dot                           Bio::Graphics::Glyph::dot
 ellipse                       Bio::Graphics::Glyph::ellipse
 extending_arrow               Bio::Graphics::Glyph::extending_arrow
 generic                       Bio::Graphics::Glyph::generic
 graded_segments               Bio::Graphics::Glyph::graded_segments
 heterogeneous_segments        Bio::Graphics::Glyph::heterogeneous_segments
 idiogram                      Bio::Graphics::Glyph::idiogram
 image                         Bio::Graphics::Glyph::image
 line                          Bio::Graphics::Glyph::line
 primers                       Bio::Graphics::Glyph::primers
 processed_transcript          Bio::Graphics::Glyph::processed_transcript
 rndrect                       Bio::Graphics::Glyph::rndrect
 ruler_arrow                   Bio::Graphics::Glyph::ruler_arrow
 segments                      Bio::Graphics::Glyph::segments
 span                          Bio::Graphics::Glyph::span
 toomany                       Bio::Graphics::Glyph::toomany
 trace                         Bio::Graphics::Glyph::trace
 transcript                    Bio::Graphics::Glyph::transcript
 transcript2                   Bio::Graphics::Glyph::transcript2
 translation                   Bio::Graphics::Glyph::translation
 triangle                      Bio::Graphics::Glyph::triangle
 wormbase_transcript           Bio::Graphics::Glyph::wormbase_transcript
 xyplot                        Bio::Graphics::Glyph::xyplot

The "perldoc" command is handy for reading the documentation from the Unix command line. For example:

  perldoc Bio::Graphics::Glyph::primers

This will provide you with a summary of the options that apply to the "primers" glyph.

In the manual pages, the glyph options are presented the way they are called from Perl. For example, the documentation will tell you to use the -connect_color option to set the color to use when drawing the line that connects the two inward pointing arrows in the primer pair glyph. This translates to the configuration file as an option named "connect_color". For example:

[PCR Products]
glyph = primer
connect_color = blue

When referring to colors, you can use a variety of color names such as "blue" and "green". To get the full list, cut and paste the following magic incantation into the command line:

perl -MBio::Graphics::Panel -e 'print join "\n",Bio::Graphics::Panel->color_names'

or see this URL:

 http://www.wormbase.org/db/seq/gbrowse?help=annotation

Alternatively, you can use the #RRGGBB notation to specify the red, green and blue components of the color. Refer to any book on HTML for the details on using the notation.

Adding features to the overview

You can make any set of tracks appear in the overview by creating a stanza with a title of the format [<label>:overview], where <label> is any unique label of your choice. The format of the stanza is identical to the others, but the indicated track will appear in the overview rather than as an option in the detailed view. For example, this stanza adds to the overview a set of features of method "gene", source "framework":

[framework:overview]
feature       = gene:framework
label         = 1
glyph         = generic
bgcolor       = lavender
height        = 5
key           = Mapped Genes

Similarly, you can make a track appear in the region panel by appending ":region" to its name:

[genedensity:region]
feature       = gene_density
glyph         = xyplot
graph_type    = boxes
scale         = right
bgcolor       = red
fgcolor       = red
height        = 20
key           = SNP Density

Semantic Zooming

Sometimes you will want to change the appearance of a track when the user has zoomed out or zoomed in beyond a certain level. To indicate this, create a set of "length qualified" stanzas of format [<label>:<zoom level>], where all stanzas share the same <label>, and <zoom level> indicates the minimum size of the region that the stanza will apply to. For example:

 [gene]
 feature = transcript:curated
 glyph    = dna
 fgcolor  = blue
 key      = genes
 citation = example semantic zoom track

 [gene:500]
 feature = transcript:curated
 glyph   = transcript2

 [gene:100000]
 feature = transcript:curated
 glyph   = arrow

 [gene:500000]
 feature = transcript:curated
 glyph   = generic

This series of stanzas says to use the "transcript2" glyph when the segment being displayed is 500 bp or longer, to use the "arrow" glyph when the segment being displayed is 100,000 bp or longer, and the "generic" glyph when the region being displayed is 500,000 bp or longer. For all other segment lengths (1 to 499 bp), the ordinary [gene] stanza will be consulted, and the "dna" glyph will be displayed. The bare [gene] stanza is used to set all but the "feature" options for the other stanzas. This means that the fgcolor, key and citation options are shared amongst all the [gene:XXXX] stanzas, but the "feature" option must be repeated.

You can override any options in the length qualified stanzas. For example, if you want to change the color to red in when displaying genes on segments between 500 and 99,999 bp, you can modify the [gene:500] stanza as follows:

 [gene:500]
 feature = transcript:curated
 glyph   = transcript2
 fgcolor = red

It is also possible to display different features at different zoom levels, although you should handle this potentially confusing feature with care.

If you wish to turn off a track entirely, you can use the "hide" flag to hide the track when the display exceeds a certain size:

 [6_frame_translation:50000]
 hide = 1

Computed Options

Some options can be computed at run time by using Perl subroutines as their values. These are known as "callbacks." Currently this works with the values of the "link", "title", "link_target", "header" and "footer" options, and any glyph-specific option that appears in a track section.

You need to know the Perl programming language to take advantage of this. The general format of this type of option is:

 option name = sub {
             some perl code;
             some more perl code;
             even more perl code;
             }

The value must begin with the sequence "sub {" in order to be recognized as a subroutine declaration. After this, you can have one or more lines of Perl code followed by a closing brace. Continuation lines must begin with whitespace.

When the browser first encounters an option like this one, it will attempt to compile it into Perl runtime code. If successful, the compiled code will be stored for later use and invoked whenever the value of the option is needed. (Otherwise, an error message will appear in your server error log).

For options of type "footer" and "header", the subroutine is passed no arguments. It is expected to produce some HTML and return it as a string value.

For glyph-specific features, such as "bgcolor" the subroutine will be called at run time with five arguments consisting of the feature, the name of the option, the current part number of the feature, the total number of parts in this feature, and the glyph corresponding to the feature. Usually you will just look at the first argument. The return value is treated as the value of the corresponding option. For example, this bgcolor subroutine will call the feature's primary_tag() method, and return "blue" if it is an exon, "orange" otherwise:

 bgcolor = sub {
         my $feature = shift;
         return "blue" if $feature->primary_tag eq 'exon';
         return "orange";
         }

See the manual page for Bio::DB::GFF::Feature for information on how to interrogate the feature object.

For special effects, such as coloring the first and last exons differently, you may need access to all five arguments. Here is an example that draws the first and last parts of a feature in blue and the rest in red:

  sub {
        my($feature,$option_name,$part_no,$total_parts,$glyph) = @_;
        return 'blue' if $part_no == 0;                # zero-based indexing!
        return 'blue' if $part_no == $total_parts-1;   # zero-based indexing!
        return 'red';
        }

If you need access to information in the parent of the feature (e.g. in a multipart feature), you can call the glyph's parent_feature() method:

 sub {
        my($feature,$option_name,$part_no,$total_parts,$glyph) = @_;
        my $parent = $glyph->parent_feature;
        return 'blue' if $parent->name =~ /Blue\d+/;
        return 'red';
        }

The parent_feature() method was added to Bioperl on 17 April 2008. If you are using an earlier version, parent_feature() will not be available.

See the Bio::Graphics::Panel manual page for more details.

Callbacks for the "link", "title", and "link_target" options have a slightly different call signature. They receive three arguments consisting of the feature, the Bio::Graphics::Panel object, and the Bio::Graphics::Glyph object corresponding to the current track within the panel:

 link = sub {
            my ($feature, $panel, $track) = @_;
            ... do something
            }

Ordinarily you will only need to use the feature object. The other arguments are useful to look up panel-specific settings such as the pixel width of the panel or the state of the "flip" setting:

 title = sub {
         my ($feature,$panel,$track) = @_;
         my $name = $feature->display_name;
         return $panel->flip ? "$name (flipped)" : $name;
      }

Named Subroutine References

If you use a version of BioPerl after April 15, 2003, you can also use references to named subroutines as option arguments. To use named subroutines, add an init_code section to the [GENERAL] section of the configuration file. init_code should contain nothing but subroutine definitions and other initialization routines. For example:

 init_code = sub score_color {
               my $feature = shift;
               if ($feature->score > 50) {
                 return 'red';
               } else {
                 return 'green';
               }
             }
             sub score_height {
               my $feature = shift;
               if ($feature->score > 50) {
                 return 10;
               } else {
                 return 5;
               }
             }

Then simply refer to these subroutines using the \&name syntax:

   [EST_ALIGNMENTS]
   glyph = generic
   bgcolor = \&score_color
   height  = \&score_height

You can declare global variables in the init_code subroutine if you use "no strict 'vars';" at the top of the section:

   init_code = no strict 'vars';
               $HEIGHT = 10;
               sub score_height {
                 my $feature = shift;
                 $HEIGHT++;
                 if ($feature->score > 50) {
                   return $HEIGHT*2;
                 } else {
                   return $HEIGHT;
                 }
               }

Due to the way the configuration file is parsed, there must be no empty lines in the init_code section. Either use comments to introduce white space, or "use" a .pm file to do anything fancy.

Subroutines that you define in the init_code section, as well as anonymous subroutines, will go into a package that changes unpredictably each time you load the page. If you need a predictable package name, you can define it this way:

  init_code = package My; sub score_height { .... }

  [EST_ALIGNMENTS]
  height = \&My::score_height

Declaring New Aggregators

The Bio::DB::GFF data model recognizes a single-level of "grouping" of features, but doesn't specify how to use the group information to correctly assemble the various individual components into a biological object. Aggregators are used to assemble this information. For example, let's say that you decide that your preferred "transcript" data model contains three subfeature types: a set of one or more features of method "exon", a single feature of method "TSS", and a single feature of method "polyA". Optionally, the data model could contain a single "main subfeature" that runs the length of the entire transcript. We might give this feature a method of "primary_transc" (for "primary transcript.")

In a GFF file, a three-exon transcript might be represented as follows:

Chr1 confirmed primary_transc 100 500  .  +  .  Transcript "ABC.1"
Chr1 confirmed TSS            100 100  .  +  .  Transcript "ABC.1"
Chr1 confirmed exon           100 200  .  +  .  Transcript "ABC.1"
Chr1 confirmed exon           250 300  .  +  .  Transcript "ABC.1"
Chr1 confirmed exon           400 500  .  +  .  Transcript "ABC.1"
Chr1 confirmed polyA          500 500  .  +  .  Transcript "ABC.1"

To aggregate this, you would like to create an aggregator named "transcript", whose "main method" is "primary_transc", and whose "sub methods" are "TSS," "exon," and "polyA."

The way to indicate this in the configuration file is to add a "complex aggregator" to the list of aggregators:

 aggregators = transcript{TSS,exon,polyA/primary_transc}

The format of this value is "aggregator_name{submethod1,submethod2,.../mainmethod}".

You can now use the name of the aggregator name as the argument of the "feature" option in a track section:

 [Transcripts]
 feature      = transcript
 glyph        = segments
 bgcolor      = wheat
 fgcolor      = black
 height       = 10
 key          = Transcripts

If you do not have a main subfeature, leave off the "/mainmethod". For example:

 aggregators = transcript{TSS,exon,polyA}

A few formatting notes. You are free to mix simple and complex aggregators in the "aggregator" option. For example, you can activate the standard "clone" and "alignment" aggregators as well as the new transcript aggregator with a line like this one:

aggregators = clone
              transcript{TSS,exon,polyA/primary_transc}
              alignment

If the complex aggregator contains whitespace or apostrophes, you must surround it with double-quotes, like this:

  "transcript{TSS,5'UTR,3'UTR,exon,polyA/primary_transc}"

Be aware that some glyphs look for particular method names when rendering aggregated features. For example, the standard "transcript" glyph is closely tied to the "transcript" aggregator, and looks for submethods named "intron", "exon" and "CDS", and a main method named "transcript."

Here is the list of available predefined aggregators:

    alignment
    clone
    coding
    transcript
    none
    orf
    waba_alignment
    wormbase_gene

To view the documentation for any of these aggregators, run the command "perldoc Bio::DB::GFF::Aggregator::aggregator_name", where "aggregator_name" is the name of the aggregator.

Grouping Features

gbrowse recognizes the concept of a "group" of related features that are connected by dotted lines. The canonical example is a pair of ESTs that are related by being from the two ends of the same cDNA clone. However many feature databases, including the GFF database recommended for gbrowse, do not allow for arbitrary hierarchical grouping. To work around this, you may specify a feature name-based regular expression that will be used to trigger grouping.

It works like this. Say you are working with EST feature pairs and they follow the nomenclature 501283.5 and 501283.3, where the suffix is "5" or "3" depending on whether the read was from the 5' or 3' ends of the insert. To group these pairs by a dotted line, specify the "group_pattern" option in the appropriate track section:

     group_pattern =  /\.[53]$/

At render time, gbrowse will strip off this pattern from the names of all features in the EST track and group those that have a common base name. Hence 501283.5 and 501283.3 will be grouped together by a dotted line, because after the pattern is removed, they will share the same common name "501283".

This works for all embedded pattern, provided that stripping out the pattern results in related features sharing the same name. For example, if the convention were "est.for.501283" and "est.rev.501283", then this grouping pattern would have the desired effect:

     group_pattern = /\.(for|rev)\./

Don't forget to escape regular expression meta-characters and to consider the various ways in which the regular expression might break. It is entirely possible to create an invalid regular expression, in which case gbrowse will crash until you comment out the offending option.

Controlling the gbrowse_details page

If a track definition's "link" option (see section B2) is set to AUTO, the gbrowse_details script will be invoked when the user clicks on a feature contained within the track. This will generate a simple table of all feature information available in the database. This includes the user-defined tag/value attributes set in Column 9 of the GFF for that feature.

You can control, to some extent, the formatting of the tag value table by providing a configuration stanza with the following format:

 [feature_type:details]
 tag1 = formatting rule
 tag2 = formatting rule
 tag3 = formatting rule

"feature_type" is the type of the feature you wish to control. For example, "gene:sgd" or simply "gene". You may also specify a feature_type of "default" to control the formatting for all features. "tag1", "tag2" and so forth are the tags that you wish to control the formatting of. The tags "Name," "Class", "Type", "Source", "Position", and "Length" are valid for all features, while "Target" and "Matches" are valid for all features that have a target alignment. In addition, you can use the names of any attributes that you have defined. Tags names are NOT case sensitive, and you may use a tag named "default" to define a formatting rule that is general to all tags (more specific formatting rules will override less specific ones).

A formatting rule can be a string with (possible) substitution values, or a callback. If a string, it can contain one or more of the substitution variable "$name", "$start", "$end", "$stop", "$strand", "$method", "$type", "$description" and "$class", which are replaced with the corresponding values from the current feature. In addition, the substitution variable "$value" is replaced with the current value of the attribute, and the variable "$tag" is replaced with the current tag (attribute) name. HTML characters are passed through.

For example, here is a simple way to boldface the Type field, italicize the Length field, and turn the Notes into a Google search:

 [gene:details]
 Type   = <b>$value</b>
 Length = <b>$value</b>
 Note  = <a href="http://www.google.com/search?q=$value">$value</a>

If you provide a callback, the callback subroutine will be invoked with three arguments. WARNING: the three arguments are different from the ones passed to other callbacks, and consist of the tag value, the tag name, and the current feature:

 Note = sub {
            my($value,$tag_name,$feature) = @_;
            do something....
            }

You can use this feature to format sequence attributes nicely. For example, if your features have a Translation attribute which contains their protein translations, then you are probably unsatisified with the default formatting of these features. You can modify this with a callback that word-wraps the value into lines of at most 60 characters, and puts the whole thing in a <pre> section.

[gene:details]
Translation = sub {
               my $value = shift;
               $value =~ s/(\S{1,60})/$1\n/g;
               "<pre>$value</pre>";
            }

Linking out from gbrowse_details

The formatting rule mechanism described in the previous section is the recommended way of creating a link out from the gbrowse_details page. However, an older mechanism is available for backward compatibility.

To use this legacy mechanism, create a stanza header named [TagName:DETAILS], where TagName is the name of the tag (attribute name) whose values you wish to turn into URLs, and where DETAILS must be spelled with capital letters. Put the option "URL" inside this stanza, containing a string to be transformed into the URL.

For example, to link to a local cgi script from the following GFF line:

IV     curated exon    518     550     . + .   Transcript B0273.1; local_id 11723

one might add the following stanza to the configuration file:

   [local_id:DETAILS]
   URL   = http://localhost/cgi-bin/localLookup.cgi?tag=$tag;id=$value

The URL option's value should be a URL containing one or more variables. Variables begin with a dollar sign ($), and are replaced at run time with the information relating to the selected feature attribute. Recognized variables are:

    $tag        The "tag" of the tag/value pair
    $value      The "value" of the tag/value pair

The value of URL can also be an anonymous subroutine, in which case the subroutine will be invoked with a two-element argument list consisting of the name of the tag and its value. This example, provided by Cyril Pommier, will convert Dbxref tags into links to NCBI, provided that the value of the tag looks like an NCBI GI number:

[Dbxref:DETAILS]
URL = sub {
      my ($tag,$value)=@_;
      if ($value =~ /NCBI_gi:(.+)/){
       return "http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=$1";
       }
       return;
     }

Configuring Balloon Tooltips

GBrowse can display popup balloons when the user hovers over or clicks on a feature. The balloons can display arbitrary HTML, either provided in the config file, or fetched remotely via a URL. You can use this feature to create multiple choice menus when the user clicks on the feature, to pop up images on mouse hovers, or even to create little embedded query forms. See http://mckay.cshl.edu/balloons.html for examples.

In the config file for the database you wish to modify, set "balloon tips" to a true value:

     [GENERAL]
     ...
     balloon tips = 1

Then add "balloon hover" and/or "balloon click" options to the track stanzas that you wish to add buttons to. You can also place these options in [TRACK DEFAULTS] to create a default balloon.

"balloon hover" specifies HTML or a URL that will be displayed when the user hovers over a feature. "balloon click" specifies HTML or a URL that will appear when the user clicks on a feature. The HTML can contain images, formatted text, and even controls. Examples:

 balloon hover = <h2>Gene $name</h2>
 balloon click = <h2>Gene $name</h2>
                 <a href='http://www.google.com/search?q=$name'>Search Google</a><br>
                 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&term=$name'>Search NCBI</a><br>

Alternatively, you can populate the balloon using data from an HTML page or dynamic CGI script running on the same server as GBrowse. This uses AJAX; it can often speed up page loading by reducing the amount of text that must be downloaded by the client. To dynamically load the balloon contents from the server, use a balloon hover or balloon click option like this:

 balloon click = /cgi-bin/get_gene_data?gene=$name

In this case, when the user clicks on the feature, it creates a balloon whose content contains the HTML returned by the CGI script "get_gene_data". GBrowse knows that this is a URL rather than the contents of the balloon by looking for the leading slash. However, to reduce ambiguity, we recommend that you prefix the URL with "url:" as so:

 balloon click = url:/cgi-bin/get_gene_data?gene=$name

This also allows you to refer to relative URLs:

 balloon click = url:../../get_gene_data?gene=$name

It is also possible to fill the balloon with content from a remote source. Simply specify a full URL beginning with "http:" "https:" or "ftp:"

balloon hover = http://www.wormbase.org/db/get?name=$name;class=gene

Note that the balloon library uses an internal <iframe> to populate the balloon with the content of external URLs. This means that vertical and horizontal scrollbars will appear if the content is too large to be contained within the balloon. If the formatting does not look right, you can design a custom balloon of the proper size as described in the next section.

The usual option value substitution rules ($name, $start, etc) work with balloons, as do callbacks. GBrowse will automatically escapes single (') and double (") quotes in the values returned by the "balloon hover" and "balloon click" options so that you don't have to worry about them messing up the HTML.

You might also wish to specify "titles are balloons" in the [GENERAL] section:

 [GENERAL]
 titles are balloons = 1

This will generate balloons on all mouse hover events, using the content that would otherwise have been placed in the built-in browser tooltip.

There is a limited amount of balloon customization that you can perform within the [track] section. If you wish the balloon to be sticky (require the user to press the close button) even if it is a hover balloon, then place this option in the [track section]:

 balloon sticky = 1

Setting "balloon sticky" to 0 will have the effect of making balloons disappear as soon as the mouse leaves them, even if it was created by a mouse click event.

If you are displaying content from a remote web or FTP server and you do not like the height of the balloon, you can adjust the height with the "balloon height" option:

 balloon height = 400

Customizing Balloons

GBrowse supports multiple balloons with different shapes, sizes, background images and timing properties. There is one built-in balloon, named "balloon", which should meet most peoples' needs. However, you can configure any number of custom balloons.

To declare two new balloons, create a "custom balloons" option in the [GENERAL] section:

custom balloons = [blue_balloon]
                  images   =  /gbrowse/images/blue_balloons
                  maxWidth = 300
                  shadow   = 0

                  [wide_balloon]
                  maxWidth = 800

This creates two new balloons. The first, named "blue_balloon" will look for its images and icons at the local URL /gbrowse/images/blue_balloons. It will have a maximum width of 300 pixels, and will cast no shadow. The second, named "wide_balloon" takes all the defaults for the default balloon, including the location of its images in the directory /gbrowse/images/balloons, except that it has a maximum width of 800 pixels. The various balloon options are described well at http://www.gmod.org/wiki/index.php/Popup_Balloons.

To use the blue balloon rather than the standard one, format the "balloon hover" and/or "balloon click" options like this:

 balloon click = [blue_balloon] /cgi-bin/get_gene_data?gene=$name

The [blue_balloon] keyword tells gbrowse to use the blue balloon for clicks on these features. The standard balloon is called "balloon", and so the following two options are equivalent:

 balloon click = /cgi-bin/get_gene_data?gene=$name
 balloon click = [balloon] /cgi-bin/get_gene_data?gene=$name

The images for custom balloons reside in the default location of /gbrowse/images/balloons, unless indicated otherwise using the "images" config option. To use custom balloon images, point "images" to a a web-accessible directory in your document tree which contains the seven PNG images described at http://www.gmod.org/wiki/index.php/Popup_Balloons. These images must be named as follows:

 balloon.png     down_right.png  up_right.png
 balloon_ie.png  down_left.png   up_left.png
 close.png

Tips for creating these images can be found at the www.gmod.org WIKI described earlier.

Generating Static Images: PNGs, SVGs and PDFs

GBrowse can create three types of static image suitable for incorporation into posters, publications or other web pages:

• PNG -- a bitmapped format suitable for low-resolution graphics, such as web pages.
• SVG -- an editable vector-graphics format, suitable for posters, publications and other high-resolution applications.
• PDF -- the familiar document exchange format, suitable for posters, publications and other high-resolution applications.

All the work is handled by the gbrowse_img script and needs little configuration. When the user selects a region and set of tracks to browse, the "link to image" and "high-res image" links at the top of the page will be automatically set to reproduce the user's view as closely as possible. GBrowse_img customization options, including instructions on how to embed an image in a web page so that the clickable imagemap links are maintained, can be found here.

The PNG generation will work in the default installation. In order to get SVG generation to work, you will need to install the perl SVG and GD::SVG modules, available from CPAN.

For PDF generation, you will need the perl GD and GD::SVG modules installed, as well as a helper application called Inkscape. Inkscape provies a command-line tool that will convert SVG files into PDF. To install, download and install it somewhere on the standard system path (e.g. /usr/bin). You will then need to create two subdirectories in the web user's home directory in order for inkscape to work properly. Assuming that the web user is "www-data" run the following commands:

sudo mkdir ~www-data/{.inkscape,.gnome2}
sudo chown www-data ~www-data/{.inkscape,.gnome2}

This will create the two directories ".inkscape" and ".gnome2" in the www-data user's home directory, and make them writable by the www-data user.

Unfortunately, Inkscape will generate a one line warning into the server error log every time it executes:

(inkscape:28490): Gdk-CRITICAL **: gdk_display_list_devices: assertion `GDK_IS_DISPLAY (display)' failed

At the current time there is no known fix for this problem.

Note that Inkscape PDF generation should work properly on all platforms, including Linux, Mac OSX and Windows. However, it has only been tested on Linux platforms at the current time.