Python bindings for the HiGlass viewer
Project description
HiGlass Python
Python bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.
This package provide access to:
- server: a lightweight flask server
- tilesets: tileset API
- client: an API for generating view configs
- viewer: an API for launching HiGlass in Jupyter Notebook or Lab
Requirements
Installation
First install higlass-python via pip:
pip install higlass-python
Jupyter notebook integration
Open a terminal and execute the following code to activate the integration:
# The following is only required if you have not enabled the ipywidgets nbextension yet
jupyter nbextension enable --py --sys-prefix widgetsnbextension
jupyter nbextension install --py --sys-prefix higlass
jupyter nbextension enable --py --sys-prefix higlass
Jupyter notebook integration
Open a terminal and execute the following code to activate the integration:
# The following is only required if you have not enabled the jupyterlab manager yet
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install higlass-jupyter
Getting started
Take a look at notebooks/Examples.ipynb on how to get started.
Development
-
Install the package in editable mode. (The module will be imported from the development directory, rather than copied to
site-packages).pip install -e .
-
Build and enable the Jupyter Notebook Extension. (With the
--symlinkoption, the assets inhiglass/staticare linked to the extension registry rather than copied.)python setup.py jsdeps jupyter nbextension enable --py --sys-prefix widgetsnbextension jupyter nbextension install --py --symlink --sys-prefix higlass jupyter nbextension enable --py --sys-prefix higlass
-
Uninstall the Jupyter Notebook Extension
jupyter nbextension uninstall --py --sys-prefix higlass
-
Experimental: install the Jupyter Lab Extension
cd js && jupyter labextension link .
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