bdgenomics.mango.pileup
Project description
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 >2.0. 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 jupyter lab:
$ 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 >= 4.0)):
$ git clone https://github.com/bdgenomics/mango
$ cd mango-pileup
$ 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]
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.
To install the JupyterLab extension, install the Package, the Jupyter widgets extension, and the bdgenomics.mango.pileup 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
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