bdgenomics.mango.pileup

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

Installation

from pip:

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

from Source:

For a development installation (requires npm >= 3.10.10 and node.js >= 6.11.0),

$ git clone https://github.com/bdgenomics/mango
$ cd mango-viz
$ rm -r bdgenomics/mango/pileup/static

Install bdgenomics.mango.pileup:

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

After pileup.js is installed once, you can just run the following for development:

$ cd mango-viz
$ rm -r bdgenomics/mango/pileup/static/
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup

For running examples:

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

For javascript development type checking:

$ cd js
$ npm run test