jbrowse-plugin-desktop-tools

A plugin that can run command line tools to prepare data for JBrowse 2.

NOTE:

This plugin can only be run with the desktop distribution of JBrowse 2.

Install

Prerequisites

Ensure you have JBrowse desktop installed.

Ensure you have bcftools installed (brew install bcftools or sudo apt install bcftools).

Ensure you have tabix installed (brew install htslib or sudo apt install htslib).

Locally

Clone the git repo, yarn, and start:

git clone https://github.com/GMOD/jbrowse-plugin-desktop-tools.git
cd jbrowse-plugin-desktop-tools
yarn
yarn start

Add to the "plugins" of your JBrowse config (your .jbrowse file):

  "plugins": [
    {
      "name": "DesktopTools",
      "url": "http://localhost:9000/dist/jbrowse-plugin-desktop-tools.umd.development.js"
    }
  ],

or navigate to the Plugin Store within JBrowse desktop and click the "Add Custom Plugin" button at the top of the store.

Then enter in the same information as highlighted in the codeblock above.

Usage

This plugin adds a new add track workflow.

1. Navigate: Add > Linear genome view > Open > Open track selector > + icon button > Add track

2. In the topmost dropdown menu select "Raw variant track".

3. Choose a local .vcf file to process

4. Change the name if relevant

5. Press "submit" and your VCF file will have been sorted, indexed, and zipped for usage within JBrowse

If your .vcf file fails to process, ensure you have all necessary prerequisites and try again.