The JBrowse biodb-to-json.pl Configuration File

biodb-to-json.pl and prepare-refseqs.pl can use a configuration file to connect to an existing Bio::DB::* database and batch-format its data for use by JBrowse You don't necessarily need a config file if all of your data is in flat files. In this case, it is recommended that you format your data using flatfile-to-json.pl. See docs/examples/format_tomato.sh for an example of a simple shell script that uses prepare-refseqs.pl and flatfile-to-json.pl to to create a complete genome browser for Tomato.

The basic syntax of the configuration file is JSON. Many of the configuration keys are quite similar to those used by GBrowse.

The root level of the config file:

key	value	type
description	Brief description of the data source	string
db_adaptor	Perl class that implements Bio::DasI. Common ones include Bio::DB::SeqFeature::Store Bio::DB::GFF Bio::DB::Das::Chado	string
db_args	arguments to the constructor for the specified db_adaptor	dictionary of key-value pairs
TRACK DEFAULTS	default track settings	track settings dictionary
tracks	settings for all the tracks	array of track settings dictionaries

The main part of the configuration file consists of the per-track settings:

key	value	type
track	track identifier used by the software. It's more convenient if this doesn't have any weird characters or spaces in it	string
key	Human-readable label for the track	string
feature	List of feature types to put into the track	array of strings
autocomplete	If you want to be able to search for the features in this track, set this to one of the following strings: label to search on the feature label alias to search on the feature aliases all to search on both labels and aliases	string
class	The CSS class for the feature. Look in the feature glyph list for the available options.	string
category	The category this track is in, for grouping the tracks together	string
urlTemplate	Template for a URL to visit if the user clicks on a feature in this track	string
extraData	Extra per-feature information to send to the client; useful in the urlTemplate	dictionary of header -> perl sub
subfeatureClasses	Specifies what CSS class to apply to what type of subfeature	dictionary of type -> CSS class
arrowheadClass	CSS class for arrowheads	string
clientConfig	settings to control the behavior of the client for this track, mainly zoom thresholds for when to display more information	dictionary