igv.js Jupyter Extension

This is an extension for Jupyter Notebook which integrates igv.js, an embeddable interactive genome visualization component written in JavaScript and CSS. It is based on the Integrative Genomics Viewer (IGV), and developed by the same team.

Installing

This extension can be installed through pip or conda.

pip install igv

or

conda install -c igv igv

Enabling

This extension can be enabled in Jupyter Notebook by running the following on the command line:

jupyter nbextension install --py igv

jupyter nbextension enable --py igv

Using the extension

This extension consists of a Python package that wraps igv.js functionality and an nbextension that's used for rendering igv.js when it is displayed in a notebook. Once the extension is installed and enabled, it can be used by importing IGV and associated classes, then returning them in a cell. Example code:

from igv import IGV, Reference, Track

IGV(locus="chr1:155,160,475-155,184,282", reference=Reference(id="hg19"), tracks=[Track(
    name="Genes", 
    url="//s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed",
    index_url="//s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed.idx", 
    display_mode="EXPANDED")])

Server

If using the built-in Jupyter webserver take note of the "Range" header requirements desribed here: Server Requirements. In general you will be restricted to serving non-indexed annotation (bed, gff) and wig files from the Jupyter web server.

Troubleshooting

error: can't copy 'igv/static/igvjs/img': doesn't exist or not a regular file

If you see the above error when trying to install through PIP, you may be experiencing a known issue with Python 2.7.6. To get around this error we recommend either updating your system's version of Python or simply installing through the conda package manager (described above).