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GBrowse 1 Configuration HOWTO

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This document provides information on configuring version 1 of the Generic Genome Browser (GBrowse), part of the GMOD Project. For version 2, see GBrowse 2 Configuration HOWTO.

Creating Databases From Scratch

GBrowse uses adaptors to read genomic data. Several of those adaptors read data from database management systems ( a.k.a. databases). If you have a significant amount of data (and most people do) then you want to store your GBrowse data in a database and use a database adaptor. Often the first step after installing GBrowse is to get the genomic data you want to see into a database that GBrowse can read.

There are 3 widely used GBrowse Adaptors that use databases:

  1. GFF3 databases - slightly faster than GFF2 and able to represent multilevel features.
  2. GFF2 databases - older and unable to represent genes with alternative splicing patterns, features with more than one level of nesting, and several other common situations. GFF2 is deprecated and if possible you are strongly encouraged to use GFF3.
  3. Chado databases - These are significantly slower than the GFF databases, but are feature-rich.


Here is the sequence of steps for creating new GBrowse databases:

  1. Make a GFF3 file for your genome (i.e. from a GenBank download that ends in .gb) - On the command line:
    bp_genbank2gff3.pl -noCDS -s antgenome.gb
    This will result in the creation of a file ("antgenome.gb.gff" in the example)
  2. Create a database in your MySQL database (e.g. antgenome) and grant the www user SELECT privileges on that database. This would be "nobody" on most systems. On Ubuntu Linux the user would be "www-data". Also, grant your own user privileges on that database.
    mysql -uroot -prootpassword
    mysql> create database antgenome;
    mysql> GRANT SELECT ON antgenome to 'www-data'@'localhost';
    mysql> GRANT ALL PRIVILEGES ON antgenome TO 'myuser'@'localhost';
    mysql>quit
  3. Copy an existing configuration file (database_name.conf) and adjust the paths to your new database and rename accordingly.
    sudo cp mysillygenome.conf /etc/gbrowse2/antgenome.conf
  4. Load the .GFF file into the database - On the command line:
    bp_seqfeature_load.pl -c --dsn "dbi:mysql:antgenome" --user "myuser" --password "my password" antgenome.gb.gff
    • If you want to change things easily in your database to display new tracks, I found it easiest to edit the .gb file. I would copy & paste specific sections (i.e. section for CDS or gene, etc. - any type can be altered) and then change the type to some key word (this becomes the "feature" in the .conf file). Then I would remake the GFF file and reload the database. This was the simplest way I had of manipulating the files to create custom tracks.

Adding and Configuring Databases

Each data source has a corresponding configuration file in the directory gbrowse.conf. Once you've created and loaded a new database, you should make a copy of one of the existing configuration files and modify it to meet your needs. The name of the new configuration file must follow the form:

 sourcename.conf

where "sourcename" is a short word that describes the data source. You can use this name to select the data source when linking to the browser. Just construct a URL that uses "sourcename" as a virtual directory under cgi-bin/gbrowse:

 http://localhost/cgi-bin/gbrowse/sourcename/

(Note: If you don't add the slash at the end, gbrowse will automatically do it for you, since the terminal slash is needed to work around an apparent bug in MSIE's cookie handling.)

It is suggested that you use the same name as the database, although this isn't a requirement. (If no "source=" argument is given, gbrowse picks the first configuration file that occurs alphabetically; you can control this by placing numbers in front of the configuration file, as in "01.yeast.conf".)

The configuration file is divided into a number of sections, each one introduced by a [SECTION TITLE]. The [GENERAL] section contains settings that are applicable to the entire application. Other sections define tracks to

You should begin with one of the example configuration files provided with the distribution (for example, the yeast configuration file ) and modify it to suit your needs.

Configuration File layout

GBrowse configuration files are arranged into configuration stanzas, or sections in the form:

# This line is a comment that will be ignored
[CONFIG ITEM]
option1 = value1
option2 = value2
etc...
  • While configuration files are being parsed, a new section always begins with a label in square brackets and a series of key/value pairs.
  • Values may span multiple lines
  • Comment lines beginning with the reserved character '#' are ignored when the configuration file is parsed. Any lines that begin with a pound sign (#) are considered comments and ignored.
  • Config files begin with the [GENERAL] section, which contains all fundamental configuration options (see below).
  • Note that all key value/pairs are assigned to the most recent section header, so take care to keep all related options grouped together before the start of the next section.

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

All [GENERAL] options are listed below, grouped together by function.

Adaptor Options

GBrowse Adaptors connect GBrowse to a data source. A config file specifies exactly one adaptor. Adaptor options specify which adaptor to use and what parameters to use with it.

db_adaptor
Tells GBrowse what database adaptor to use. By using different adaptors you can attach GBrowse to a variety of different databases. Available options are listed on the GBrowse Adaptors page.
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.

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.

Appearance Options

Appearance options affect what is displayed back to the user. This is related to, but different from the Behavior Options, which determines how GBrowse responds to the user. Search both this and the Behavior options sections for options that don't fall cleanly into one category or the other.

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.)
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
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
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 conversion 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.
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. The default value is 50000.
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.
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.
detailed bgcolor
This is the color for the background of the detailed view.
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>
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:

    footer = <hr>
        <table width="100%">
        <TR>
        <TD align="LEFT" class="databody">
        For the source code for this browser, see the <a href="http://gmod.org">
        Generic Model Organism Database Project.</a>  For other questions, send
        mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
        </TD>
        </TR>
        </table>
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
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."
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 3x3 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 GBrowse2 Admin Tutorial for more details.

instructions section, search section, overview section, region section, details section, tracks section, display_settings section, 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.

Option Where it goes
header between the top and the instructions
html1 between the instructions and the navigation bar
html2 between the navigation bar and the overview
html3 between the overview and the detail view
html4 between the detail view and the data source panel
html5 between the data source panel and the track list
html6 between the track list and the annotation upload
footer between the annotation upload and the bottom

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 = $main::CONFIG->tr('Go');
        return
        qq(
        <table width="800" border="0">
        <tr class="searchbody">
        <td align="left" colspan="3" />
        <b>Dump:</b><input type="button" value="Assembly" onclick="window.open('gbrowse?plugin=AssemblyDumper;plugin_action=$go');">
        <input type="button" value="Reads" onclick="window.open('gbrowse?plugin=ReadDumper;plugin_action=$go');">
        </td>
        </tr>
        </table>
        );
       }

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 Print the track labels between the tracks themselves.
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:

key Print just the key (the track label).
suppress Suppress the track completely.
line Draw a solid line across the track.
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 this email 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 PlasmoDB.

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.

Behavior Options

Behavior options affect how GBrowse responds to the user. This is related to, but different from the Appearance Options, which determine what is displayed back to the user. Search both this and the Appearance Options sections for options that don't fall cleanly into one category or the other.

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 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 the Bio::DB::SeqFeature::Store, BioSQL, or Chado adaptors.

reference class

Note: This option is used only with the Bio::DB::GFF (GFF2) adaptor.

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):

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.
merge searches
If this is set to true (the default), then features with the same name, chromosome and type will be merged into one feature during searches. If this is set to false (zero), then no merging will occur. Set this to true (1) if searches are returning many results, and to false (0) if searches are returning too few. (This option was added in version 1.70).
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.
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.
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. There is no equivalent configuration option.

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
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.
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')">
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.
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 users' previous search will not be automatically re-executed the next time they visit 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.
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 the BioDAS web site 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 sources 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.

Directory and URL Options

These options specify where GBrowse should find or put different types of files.

  • 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").

New in version 1.70: You can specify multiple stylesheets by separating them by spaces. You can also specify a media type by following this format:

 stylesheet = http://www.example.com/stylesheets/lowres.css(screen)
              http://www.example.com/stylesheets/audio.css(audio)
              http://www.example.com/stylesheets/hires.css(paper)
  • 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.


Plugin Options

Plugins are a way for third party developers to add functionality to GBrowse without changing its core source code. Plugins are stored in the GBrowse configuration directory under the plugins subdirectory. See plugins.


  • plugins

This is a list of plugins that you want to be available from gbrowse. 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.

Track Sharing Options

Users can link to their own tracks or to tracks published by other GBrowse or DAS servers. GBrowse can also integrate with Galaxy.

  • 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.

  • 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/tool_runner?tool_id=TOOL_ID


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). [TOOL_ID] will be provided by Galaxy developers.

  • 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.

  • 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

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 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.

It isn't possible to use wild-cards or pattern matching.

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.
visible (Version 1.71 and higher)
This controls the default visibility of the track, and may be one of show, hide or collapse. If present, this option overrides the visibility of tracks defined in the [general] section under default tracks.
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 & 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 GBrowse2 Admin 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

See the separate article GBrowse Configuration/Glyphs for this important topic.

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 above) 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". "tag1", "tag2", etc. 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. You may also specify a feature_type of "default" to control the formatting for all features (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

See: GBrowse Configuration/Balloons.

Generating Static Images: PNGs, SVGs and PDFs

See: GBrowse Configuration/Images.

Generating Feature Frequency Histograms

See: GBrowse Configuration/Feature frequency histograms

Internationalization

See: GBrowse Configuration/I18n.

Authentication & Authorization

See: GBrowse Configuration/Authentication.

Displaying Genetic & RH Maps

GBrowse can be tweaked to make it more suitable for displaying genetic and radiation hybrid maps.

The main issue is that the Bio::DB::GFF database expects coordinates to be positive integers, not fractions, but genetic and RH maps use floating point numbers. Working around this is a bit of an ugly hack. Before loading your data you must multiply all your coordinates by a constant power of 10 in order to convert them into integers. For example, if a genetic map uses Morgan units ranging from 0 to 1.80, you would multiple by 100 to create a map in ranging from 0 to 180.

Create a GFF file containing the markers in modified coordinates and load it as usual. Now you must tell GBrowse to reverse these changes. Enter the following options into the [GENERAL] section of the configuration file:

units = M
unit_divider = 100

These two options tell GBrowse to use "M" (Morgan) units, and to divide all coordinates by 100. GBrowse will automatically display the scale using the most appropriate units, so the displayed map will typically be drawn using cM units.


Changing the Location of the Configuration Files

If you wish to change the location of the gbrowse.conf configuration file directory, you must manually edit the gbrowse CGI script. Open the script in a text editor, and find this section:

###################################################################
# Non-modperl users should change this variable if needed to point
# to the directory in which the configuration files are stored.
#
use constant CONF_DIR => '/usr/local/apache/conf/gbrowse.conf';
#
###################################################################

Change the definition of CONF_DIR to the desired location of the configuration files.

An alternative, for users of mod_perl only, is to add the GBrowseConf per-directory variable to the configuration for the directory in which the gbrowse script lives. This variable overrides the CONF_DIR value. For example:

<Directory /usr/local/apache/cgi-perl>
  SetHandler      perl-script
  PerlHandler     Apache::Registry
  PerlSendHeader  On
  Options         +ExecCGI
  PerlSetVar      GBrowseConf /etc/gbrowse.conf
</Directory>


Using DAS (Distributed Annotation System) Databases

See: GBrowse Configuration/DAS.

The Bio::MOBY Browse

See: GBrowse Configuration/BioMOBY.

Filtering Search Results

GBrowse provides a method to filter the contents of individual tracks based on information that can be obtained from feature attributes. For example, suppose you have performed a blast and added all hits as similarity features on an entry. In gbrowse, all those features can get a little crowdy. The administrator can decide to show only the top 5 of the blast hits. This can easily be accomplished by adding the filter option in the conf file. It might look like this:

 [BLAST]
 feature       = blast
 glyph         = segments
 filter = sub {
                my $feat = shift;
                (my $rank) = $feat->get_tag_values('rank'); # persistent Bio::SeqFeature::Generic features
                #(my $rank) = $feat->attributes('rank'); # Bio::DB::GFF::Feature
                $rank < 6;
              }

Another useful example is to show features coming from a plain genbank file. When loaded into BioSQL the source becomes 'EMBL/Genbank/SwissProt'. Using the Bio::DB::Das::BioSQL adaptor you have to pass the source to the feature option. It can be rather difficult to distinguish all the features when they all have the same source string. This problem can be solved using the filter option. In the following example the difference between the features is done based on the primary_tag

 [REGION]
 feature      = EMBL/GenBank/SwissProt
 filter       = sub {
                 my $feat = shift;
                 $feat->primary_tag =~ /region/i;
                }
 key          = RefSeq Protein Domains
 [SIGPEPTIDE]
 feature      = EMBL/GenBank/SwissProt
 filter       = sub {
                 my $feat = shift;
                 $feat->primary_tag =~ /sig_peptide/i;
                }
 key          = RefSeq Signal Peptide


Invoking GBrowse URLs

See: GBrowse Configuration/URL schema.

Important Maintenance

GBrowse creates lots of cache files as it operates, and it does not garbage collect them automatically. To keep the cache files under control, you should run the following cron job at regular intervals:

        cd HTDOCS/gbrowse/tmp
        find . -type f -atime +20 -print -exec rm {} \;

Be sure to replace HTDOCS with the path to your web server HTML document root directory, and make sure that the cron job runs under has the proper permissions to delete the files in this directory.

Further Information

For further information, bug reports, etc, please consult the GMOD Mailing Lists. The main mailing list for gbrowse support is mailto:gmod-gbrowse@lists.sourceforge.net. You can also get help on the GMOD IRC channel on Freenode: irc://irc.freenode.net/#gmod

Have fun!

Lincoln Stein & the GMOD development team.