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A collection of visualizations for genomics related information for use with Jupyter notebooks.
Jupyter Notebook JavaScript Python Other
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jp_gene_viz
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README.md

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:

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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