jp_gene_viz

A collection of visualizations for genomics related information for use with Jupyter notebooks.

Please see the index.ipynb IPython notebook for a guide to the package content.

To launch a container to run the package in the Binder service, please click the image link below:

Installation

The installation requires the Python module jp_gene_viz to be installed with its dependencies and for the wigdets extension to be enabled in Jupyter/IPython.

For example the following sequence completes a first time complete installation

install prerequisites

You will need Python 2.7 and some other libraries for the installation to succeed. I recommend installing Anaconda for python 2.7 to get all needed prerequisite dependencies.

On Debian Linux without using Anaconda I needed to add the following system libraries

sudo apt-get install python-pip
sudo apt-get install python-dev
sudo apt-get install -y libigraph0-dev 
sudo apt-get install libxml2-dev
sudo apt-get install zlib1g-dev
sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran

clone the repository and change directory into the repository folder

git clone https://github.com/simonsfoundation/jp_gene_viz.git
cd jp_gene_viz

install the requirements and the module

pip install -r requirements.txt
python setup.py install

enable the widgets extension (just in case it isn't already enabled)

jupyter nbextension enable --py --sys-prefix widgetsnbextension

Note: We are upgrading the repository to work with the latest ipywidgets and iPython releases. If you have problems installing the package please post an issue at https://github.com/simonsfoundation/jp_gene_viz.

ERM