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BioJS2Galaxy – A step by step guide

By Benedikt Rauscher, Benjamen White – 12/07/2015.

To encourage the use of BioJavaScript (BioJS) visualisations in Galaxy we decided to create this simple step by step guide on how to use @MrGreenify’s application, biojs2galaxy, which he introduced at the Galaxy Community Conference 2015 in Norwich. As an example, we will use the Multiple Sequence Alignment (MSA) viewer BioJS component (which was also written by @MrGreenify).

To use biojs2galaxy you need to have node and npm installed. If you have never heard of node or npm it’s about time! You can find all the information you need in the npm documentation.

Once you have installed npm you can use it to download biojs2galaxy with the following command:

sudo npm install -g biojs2galaxy

Once the installation was successful, typing biojs2galaxy into your terminal should produce the following result:Biojs2galaxy Installation

Now you are ready to use biojs2galaxy to import BioJS visualisation plugins into your Galaxy installation.

The following command will import the MSA viewer into your Galaxy installation:

biojs2galaxy msa -o <path2galaxy>/config/plugins/visualizations/

Note: This command will import the plugin into the standard Galaxy visualisation plugin folder. If you have changed the standard configuration, please adapt it accordingly.

In the end you should see the following in your terminal:Congratulations!

Now all you need to do is restart Galaxy and you are good to go! In Galaxy, upload a file in a MSA-suited file format, select it, and click the visualisation icon. Ta da!BioJS MSA viewer in Galaxy

Not all BioJS components support a Galaxy import yet, but many do. If you want to import all available BioJS components into your Galaxy installation with one command you can use:

biojs2galaxy --all

We hope you found this short guide useful, please feel free to share it!

Published inBioJS

One Comment

  1. MJ MJ

    is there anyway to integrare biojs-vis-sam tool to galaxy?
    please help me

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