A collection of visualizations for genomics related information for use with Jupyter notebooks.
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.
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:
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
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
git clone https://github.com/simonsfoundation/jp_gene_viz.git
cd jp_gene_viz
pip install -r requirements.txt
python setup.py install
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.
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
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.