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GBrowse Configuration/URL schema
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:
Don't worry about this. The URL works the same with and without the terminal slash.
The argument "q" will set the landmark or search string:
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:
Alternatively, you can use a single q parameter and separate each landmark name with a dash:
The rules for specifying relative offsets and object classes are the same as in the main search field:
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".
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:
To use the "+" character you may have to URL escape it:
All tracks not explicitly given by the label parameter will be closed (disabled).
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:
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:
When modifying track state, the "label" parameter is processed first, followed by the "enable" parameter and the "disable" parameter.
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.
Set the width of the overview, region and details images, in pixels.
Set the length of the region covered by the "region" panel, in base pairs.
The name of a feature to highlight in the format "<feature_name>@<color_name>". Example:
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.
The name of a region to highlight in the format "<seq_id>:start..end@color". Example:
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.
The position of the key in the detail panel. Possible values are "between," "beneath," "left" and "right".
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).
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:
Pass multiple "add" parameters to upload several features. "add" can be abbreviated to "a" for terseness.
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" can be abbreviated to "s" for terseness.
If true, open up the track configuration page.
Open up the specified help page. Possible values are:
Open the general help page
Open up the track description & citation page
Open the page that describes how to generate an embedded image of the current view
The page that describes how to generate SVGs
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.
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.
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:
Plugins tend not to be well documented, so you may have to read through the source code to figure out their arguments.