https://github.com/simonsfoundation/jp_gene_viz
A collection of visualizations for genomics related information for use with Jupyter notebooks.
https://github.com/simonsfoundation/jp_gene_viz
Last synced: about 1 year ago
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A collection of visualizations for genomics related information for use with Jupyter notebooks.
- Host: GitHub
- URL: https://github.com/simonsfoundation/jp_gene_viz
- Owner: simonsfoundation
- Created: 2015-09-10T19:26:17.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2022-02-28T18:03:09.000Z (over 4 years ago)
- Last Synced: 2025-03-24T08:11:13.658Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 36.1 MB
- Stars: 10
- Watchers: 13
- Forks: 9
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
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README
# 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](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:
[](http://mybinder.org/repo/simonsfoundation/jp_gene_viz)
# 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](https://www.continuum.io/downloads) 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](https://brew.sh/) 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](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](https://github.com/simonsfoundation/jp_gene_viz).