## Installation

### PyPI

```
$ pip install jbrowse-jupyter
```

### Install with conda

Clone the GMOD/jbrowse-jupyter [repository](https://github.com/GMOD/jbrowse-jupyter) and [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html). 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 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](https://softwarejargon.com/jupyterlab-and-conda-environment-installation-and-setup/)


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

### Resources
* [Dash Applications](https://dash.plotly.com/layout) how to get started to custumize Dash applications.
* [Dash HTML components](https://dash.plotly.com/dash-html-components) Dash html components to build the Dash aplication layout.
* [DashJupyter](https://github.com/plotly/jupyter-dash) library to enable embedding Dash components in jupyter notebooks.
* [DashJbrowse](https://github.com/GMOD/dash_jbrowse) suite of Dash components for JBrowse views. (JBrowse Linear Genome View and JBrowse Circular Genome View)
* [JBrowse Docs](https://jbrowse.org/jb2/)
* [JBrowse Config Guide](https://jbrowse.org/jb2/docs/config_guide/)
* [JBrowse Views](https://jbrowse.org/jb2/download/#embedded-components)