JBrowse

Installation

1. Download the jbrowse.zip file and unzip into plugins directory.

2. Edit database details in services/settings.php file.

Manual installation from JBrowse.org - optional

Following steps are important when you need to convert existing JBrowse into GenIE module.

1. Copy JBrowse into plugins folder

2. Copy index.php into jbrowse folder

3. Create menu item called jbrowse

4. Change plugins plugins/jbrowse/main.css and plugins/jbrowse/genome.css

5. Copy pugins/jbrowse/index.html into plugins/jbrowse/tool.php from jbrowse.zip

6. Copy plugins/jbrowse/src/dojo/dojo.css from jbrowse.zip

7. Copy plugins/jbrowse/src/dijit/theme/tundra/tundra.css from jbrowse.zip

Loading data into JBrowse

bin/prepare-refseqs.pl --fasta [genome fasta file]
bin/flatfile-to-json.pl --gff [GFF3 file]] --trackLabel [Label name] --trackType CanvasFeatures
bin/generate-names.pl -v

Usage

Navigate to http://[your server name]/genie/jbrowse

For more information please go to JBrowse documentation