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:
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
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
For some Macs the
pip install of requirements fails to install
If this happens use homebrew to install the
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
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.