JBrowseΒΆ
Installation
- Download the jbrowse.zip file and unzip into plugins directory.
- 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.
- Copy JBrowse into plugins folder
- Copy
index.php
into jbrowse folder - Create menu item called jbrowse
- Change plugins
plugins/jbrowse/main.css
andplugins/jbrowse/genome.css
- Copy
pugins/jbrowse/index.html
intoplugins/jbrowse/tool.php
from jbrowse.zip - Copy
plugins/jbrowse/src/dojo/dojo.css
from jbrowse.zip - 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