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GBrowse Configuration/URL schema

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This article describes the public CGI parameters recognized by GBrowse.

For the main GBrowse configuration article, see: GBrowse Configuration.

Invoking GBrowse URLs

By setting the parameters in the URL, you can get gbrowse to do various useful things:

The source argument

The last component of the GBrowse path is the symbolic name of the data source. For example:

  http://www.your.site/cgi-bin/gbrowse/volvox
  http://www.your.site/cgi-bin/gbrowse/yeast
  http://www.your.site/cgi-bin/gbrowse/my_testing_database

These will correspond to config files named volvox.pm, yeast.pm and my_testing_database.pm respectively. As noted earlier, you can place numbers in front of the configuration file names in order to adjust the order in which they appear in the data source menu.

NOTE: For obscure reasons involving Internet Explorer compatibility, GBrowse will add an extra slash to the end of the URL, resulting in URLs that look like:

 http://www.your.site/cgi-bin/gbrowse/yeast/?q=NAB2

Don't worry about this. The URL works the same with and without the terminal slash.

q

The argument "q" will set the landmark or search string:

   http://www.your.site/cgi-bin/gbrowse/yeast?q=NAB2

This will have the same effect as typing "NAB2" into the GBrowse search box. To go immediately to the multiple hits page (which shows hits on several overview panels), use multiple q arguments:

  http://www.your.site/cgi-bin/gbrowse/yeast?q=NAB2;q=NPY1

Alternatively, you can use a single q parameter and separate each landmark name with a dash:

  http://www.your.site/cgi-bin/gbrowse/yeast?q=NAB2-NPY1

The rules for specifying relative offsets and object classes are the same as in the main search field:

  http://www.your.site/cgi-bin/gbrowse/yeast?q=Gene:NAB2:1..5000


ref, start, stop, end

Together the "ref," "start" and "stop" arguments specify the reference sequence and the start and end coordinates of the region of interest. The "q" argument, if present, overrides these settings. The "end" argument is a synonym for "stop".

label

The tracks to display. This parameter must contain the track names (i.e. the names in [brackets] in the config file) separated by "+" or "-" characters. For example:

  http://www.your.site/cgi-bin/gbrowse/yeast?label=ORFs-tRNAs

To use the "+" character you may have to URL escape it:

  http://www.your.site/cgi-bin/gbrowse/yeast?label=ORFs%2BtRNAs

All tracks not explicitly given by the label parameter will be closed (disabled).

enable

Tracks to enable. The tracks indicated by this parameter will be opened in addition to any tracks that were previously opened by the user. The format is the same as label:

  http://www.your.site/cgi-bin/gbrowse/yeast?enable=ORFs-tRNAs

disable

Tracks to close. The tracks indicated by this parameter will be disabled. Tracks not mentioned by this parameter will keep their previous state. The format is the same as label:

  http://www.your.site/cgi-bin/gbrowse/yeast?disable=ORFs-tRNAs

When modifying track state, the "label" parameter is processed first, followed by the "enable" parameter and the "disable" parameter.

flip

Whether to flip the display. If set to a true value (flip=1), then the coordinates will be reversed so that forward strand features become reverse strand features. If set to a false value (flip=0) or absent, then the forward strand is displayed as per usual.

width

Set the width of the overview, region and details images, in pixels.

region_size

Set the length of the region covered by the "region" panel, in base pairs.

h_feat

The name of a feature to highlight in the format "<feature_name>@<color_name>". Example:

     h_feat=SKT5@blue

You may omit "@color", in which case the highlight will default to yellow. You can specify multiple h_feat arguments in order to highlight several features with distinct colors. Passing an argument of h_feature=_clear_ will clear all feature highlighting.

h_region

The name of a region to highlight in the format "<seq_id>:start..end@color". Example:

     h_region=Chr3:200000..250000@wheat

You may omit "@color" in which case the highlight will default to lightgrey. You can specify multiple h_region arguments in order to highlight multiple sequence ranges with different colors. Passing an argument of h_region=_clear_ will clear all region highlighting.

ks

The position of the key in the detail panel. Possible values are "between," "beneath," "left" and "right".

sk

The sort order of track names in the "Tracks" panel. Values are "sorted" (alphabetically sorted by name) and "unsorted" (sorted by the order of tracks as defined in the config file).

add

Upload a feature and add it in its own track. The format is "reference+type+name+start..end", where reference is the landmark for the coordinates (e.g. a named gene or chromosome), type is the type of the feature, name is the name of the feature, and start..end are the start and end coordinates. For a feature that has multiple segments, you may use multiple start..end ranges, separated by commas. Example:

 add=chr3+miRNA+mir144+2309229..2309300,2309501..2309589

Pass multiple "add" parameters to upload several features. "add" can be abbreviated to "a" for terseness.

style

Specify the style for features uploaded using "add". It is a flattened version of the style configuration sections described in this document. Lines are separated by "+" symbols rather than newlines. The first word in the argument is the feature type to configure, for example "miRNA." Subsequent option=value pairs control the glyph and glyph options. For example, if you have added a "miRNA" annotation, then you can tell the renderer to use a red arrow for this glyph in this way:

  style=miRNA+glyph=arrow+fgcolor=red

"style" can be abbreviated to "s" for terseness.

track_options

If true, open up the track configuration page.

help

Open up the specified help page. Possible values are:

general

Open the general help page

citations

Open up the track description & citation page

link_image

Open the page that describes how to generate an embedded image of the current view

svg_image

The page that describes how to generate SVGs

id

The id is a unique session ID that will store persistent configuration information. You do not typically need to use the id parameter except in the circumstance in which you wish to upload an annotation file programatically, in which case you should choose some large hard-to-guess number.

Upload, upload_annotations, id:

These three arguments must be present in order to upload a file of external annotations to the server. "Upload" must be a true value, and "upload_annotations" will contain the content of the uploaded file. Note that you must POST the data using MIME type "multipart/form-data". The "id" argument is used to associated the upload with a session. Pick some long, hard to guess number. This will be associated stably with the uploaded file(s). To see the upload information, provide the same number in the "id" argument every time you access gbrowse.

eurl

Specify the URL of a remote annotation source to load into the database. You should also supply an "id" argument as well, as described earlier, in order to be able to view the annotations.

plugin, plugin_do

These arguments run plugins. The "plugin" argument gives the name of the plugin to activate. The name is the last component of the plugin package name, e.g. FastaDumper. The "plugin_do" argument selects what to do with the plugin. Possible values are "Configure", "Find" and "Go". "Configure" launches the plugin's configure page, "Go" runs dumper plugins' dump operation, and "Find" activates finder plugins' find function. For find operations, you should in most cases pass the find string in the "q" argument, but this depends on the particular plugin. Each plugin may have its own set of URL arguments. A plugin's arguments are preceded by the plugin's name. For example, the FastaDumper plugin has a parameter named "format" which controls the output format. So to invoke this plugin and make the output plain text, one would provide the arguments:

http://www.your.site/cgi-bin/gbrowse/yeast?q=NUT21;plugin=FastaDumper;
            plugin_do=Go;FastaDumper.format=text

Plugins tend not to be well documented, so you may have to read through the source code to figure out their arguments.