Installation

PyPI

$ pip install jbrowse-jupyter

Install with conda

Clone the GMOD/jbrowse-jupyter repository and install conda. Once you have conda installed, follow the steps found below to create a conda envirnment and install the dependecies.

$ cd jbrowse-jupyter
$ conda create -n myenv python=3.6
$ conda activate myenv
$ pip install -r requirements.txt

You can find examples in the root of the directory.

  • LGV - browser.py or the browser.ipynb

  • CGV - cgv_examples.py or cgv_examples.ipynb

browser.py uses the Dash library to create a python application with the Dash JBrowse LinearGenomeView component and configured with the help of this package. browser.ipynb is jupyter notebook using the JupyterDash library to embed a Dash JBrowse LinearGenomeView component in a cell. cgv_examples.py a Dash application using the Dash JBrowse CircularGenomeView component cgv_examples.ipynb is jupyter notebook using the JupyterDash library to embed a Dash JBrowse CircularGenomeView component in a cell.

To run the Python Dash application

$ python browser.py

To run the jupyter notebook Make sure you have jupyter notebook or jupyterlab.

Within the myenv conda environment

$ pip install jupyterlab

More information on using a specific environment in a jupyter notebook

For more information about Dash and Dash applications check out these articles.

Resources