bdgenomics.mango.pileup

bdgenomics.mango.pileup is a Jupyter widget that allows users to view genomic reads, variants and features in a Jupyter notebook or in Jupyter lab version >3.0.0. bdgenomics.mango.pileup builds off of pileup.js.

Installation

from pip:

$ pip install bdgenomics.mango.pileup

Enable widgets for Jupyter notebook:

$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup  # can be skipped for notebook version 5.3 and above

Install widgets for jupyterLab:

$ jupyter labextension install @jupyter-widgets/jupyterlab-manager # install the Jupyter widgets extension
$ jupyter labextension install bdgenomics.mango.pileup

Running Examples

$ First run installation, explained above.
$ cd examples
$ jupyter notebook

Or run in Jupyter lab:

$ jupyter lab

from Source:

For a development installation (requires npm (version >= 3.8) and node (version >= 12.0)):

$ git clone https://github.com/bdgenomics/mango
$ cd mango-pileup

Install bdgenomics.mango.pileup as a Jupyter Notebook Extension:

$ make clean
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup

Note for developers: the --symlink argument on Linux or OS X allows one to modify the JavaScript code in-place. This feature is not available with Windows.

Install bdgenomics.mango.pileup as a JupyterLab extension:

$ pip install -e .
$ cd bdgenomics/mango/js/
$ jupyter labextension install @jupyter-widgets/jupyterlab-manager # install the Jupyter widgets extension
$ jupyter labextension install .

Testing:

mango-pileup has a Makefile with a test command to run tests for python and javascript:

$ make test