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
$ conda activate myenv
$ pip install -r requirements.txt
You can find examples in the root of the directory.
LGV -
browser.py
or thebrowser.ipynb
CGV -
cgv_examples.py
orcgv_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
Dash Applications how to get started to custumize Dash applications.
Dash HTML components Dash html components to build the Dash aplication layout.
DashJupyter library to enable embedding Dash components in jupyter notebooks.
DashJbrowse suite of Dash components for JBrowse views. (JBrowse Linear Genome View and JBrowse Circular Genome View)