Dataset Selector · JBrowse 1

Beginning in version 1.9.0, JBrowse supports an optional dropdown dataset selector that appears in the menu bar in the upper left corner of the JBrowse display. The selector displays a list of dataset names based on the datasets key in the JBrowse configuration. When the selector is changed, a page reload is triggered, with the browser navigating to the URL associated with the selected dataset.

To set which value of the dataset selector is currently selected, the configuration variable dataset_id should be set to the name of the corresponding entry in the datasets list.

The selector is only shown if both datasets and dataset_id are set in the configuration.

Example Dataset Switching Configuration

In a global config, like jbrowse.conf, you can add the "list of datasets"

in jbrowse.conf:

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Volvox Example
[datasets.modencode]
url  = ?data=sample_data/json/modencode
name = MODEncode Example
[datasets.yeast]
url  = ?data=sample_data/json/yeast
name = Yeast Example

Then add the "dataset_id" to the tracks.conf file for your individual data directories

in sample_data/json/volvox/tracks.conf:

   [general]
   dataset_id = volvox

in sample_data/json/modencode/tracks.conf:

   [general]
   dataset_id = modencode

in sample_data/json/yeast/tracks.conf:

   [general]
   dataset_id = yeast

You can see that the dataset_id corresponds to whatever is inside the declaration, e.g. when it says [datasets.yeast], yeast is the ID.

Note that it is also possible to put the "list of datasets" in a tracks.conf file instead of the jbrowse.conf file if you prefer to store all your configs in track specific directories. Then you just paste the same "list of datasets" in all your dataset directories.

For example, having this code in tracks.conf

   [general]
   dataset_id = fish1
   [datasets.fish1]
   name = Fish genome 1.0
   [datasets.fish2]
   name = Fish genome 2.0

Will populate the dataset selector with Fish 1 and 2 and display the name of Fish 1 in the genome area. This is just in contrast to putting the datasets configuration in jbrowse.conf and the dataset_id in the individual data directories (e.g. all the datasets configs are copied to each data directory)