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jp_gene_viz

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

NOTE: THIS REPOSITORY IS DEPRECATED

This repository is deprecated because the Jupyter project no longer supports Python 2. Components of the repository use libraries which only work correctly in Python 2.

As far as I know at this writing you can still install these components into a legacy Python 2 kernel and everything will still work in classic Jupyter notebooks, but it may stop working at some future Jupyter release.

Some useful functionality from this repository has been ported to run in Python 3 with Jupyter using the jp_doodle Jupyter widget infrastructure. Please post an issue if you would like to see other features ported.

The package

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:

Binder

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.

Linux only:

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

Linux and Mac: install the requirements and the module

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

Mac notes

For some Macs the pip install of requirements fails to install python-igraph. If this happens use homebrew to install the igraph library

brew install igraph

and then run the pip install again.

Windows install

To install for windows the python-igraph package must be installed in a separate step. to to http://www.lfd.uci.edu/~gohlke/pythonlibs/#python-igraph to get python_igraph‑0.7.1.post6‑cp27‑cp27m‑win_amd64.whl and then install using a command similar to

python -m pip install Downloads\python_igraph-0.7.1.post6-cp27-cp27m-win_amd64.whl

Then install the remaining components

pip install -r windows_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.

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

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