[](https://pypi.python.org/pypi/genepattern-notebook)
[](https://travis-ci.org/genepattern/genepattern-notebook)
[](http://genepattern-notebook.org/programmatic/)
[](https://hub.docker.com/r/genepattern/genepattern-notebook/)
[](https://gitter.im/genepattern/genepattern-notebook?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
GenePattern Notebook for JupyterLab
====================
The [GenePattern Notebook](http://www.genepattern-notebook.org)
environment gives GenePattern users the ability to interleave text, graphics, and code with
their GenePattern analyses to create "notebooks" that can be edited, shared, and published.
GenePattern Notebooks are built on the [Jupyter](https://jupyter.org/) environment
and extend it so that users can take advantage of its ease of use and ability to encapsulate
an entire scientific research narrative, without the need to write code. They are a core
component of the [g2nb](https://github.com/g2nb) project.
> ### **Looking for classic Jupyter Notebook support?**
> **Jupyter Notebook support in is available, albeit no longer in active development. You can
> find it in its own branch. [Just click here!](https://github.com/genepattern/genepattern-notebook/tree/notebook)**
### **Prerequisites**
* JupyterLab >= 3.0.0
* ipywidgets >= 7.0.0
# Docker
A Docker image with nbtools and the full JupyterLab stack is available through DockerHub.
```bash
docker pull genepattern/lab
docker run --rm -p 8888:8888 genepattern/lab
```
# Installation
Full installation instructions for casual use are detailed on the
[GenePattern Notebook website](http://www.genepattern-notebook.org/install/). Users should
also consider the [g2nb Notebook Repository](https://notebook.genepattern.org), which
provides an install-free cloud deployment of the full suite of g2nb tools, including GenePattern Notebook.
## Development Install
The installation instructions below are intended for developers who want to install the
project from PIP or GitHub for the purposes of software development.
### Install Python
In order to get the GenePattern Notebook working you will first need to install a compatible
version of Python. This means you will need Python 3.6+. We recommend using the
[Anaconda](https://www.anaconda.com/download/#macos) Python distribution. This is
a scientific version of Python that ships with many of the most popular Python packages for
science, math and data analysis (ex: NumPy, SciPy, Pandas, Matplotlib, IPython, etc.).
**Note for Mac Users:** Mac comes with Python, but if you have an older version of the OS
you will need to install a newer version, as many older versions of MacOS ship with Python 2.
### Install GenePattern Notebook from GitHub
Copy the contents of genepattern-notebook/extension to your development computer and ensure
that the resulting directory if on your Python path. To test this, open Python and try to
*import genepattern*. If this is successful, you have a copy of the extension available.
If you don't already have Jupyter installed, you can install it from PIP by running:
> pip install jupyter
From here go to the "Load the GenePattern extension" step below.
### Install GenePattern Notebook from PIP or Conda
The easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by
executing one of the following commands:
```bash
pip install genepattern-notebook
```
*or*
```bash
conda install -c genepattern genepattern-notebook
```
### Load the nbtools extension
```bash
# Install ipywidgets, if you haven't already
jupyter nbextension enable --py widgetsnbextension
jupyter labextension install @jupyter-widgets/jupyterlab-manager
# Clone the nbtools repository
git clone https://github.com/genepattern/nbtools-lab-prototype.git
cd nbtools-lab-prototype
# Install the nbtools JupyterLab prototype
pip install .
jupyter labextension install .
jupyter nbextension install --py nbtools --sys-prefix
jupyter nbextension enable --py nbtools --sys-prefix
```
### Launch Jupyter
Finally, you may launch JupyterLab by issuing the following command at the terminal:
> jupyter lab
This will start up the notebook kernel and launch your web browser pointing to the Notebook.
# Related Repositories
The following GitHub repositories contain code or other data related to the GenePattern
Notebook environment.
* [g2nb](https://github.com/g2nb/g2nb): A meta-package which installs all of the g2nb tools and extensions.
* [genepattern-python](https://github.com/genepattern/genepattern-python): The GenePattern
Library allows for programmatic access to GenePattern from Python, and is used by
GenePattern Notebook behind the scenes.
* [nbtools](https://github.com/g2nb/nbtools): The Notebook Tool Manager
is a tool-agnostic interface and registry for searching, browsing and launching available
notebook tools in a Jupyter environment.
* [jupyter-wysiwyg](https://github.com/g2nb/jupyter-wysiwyg): A WYSIWYG editor for
markdown cells.
* [example-notebooks](https://github.com/g2nb/example-notebooks): A repository of example notebooks that
demonstrate functionality or analysis techniques in the GenePattern Notebook environment.
* [workspace](https://github.com/g2nb/workspace): Scripts, services
and other infrastructure used in the operation of the GenePattern Notebook Repository.
# Known Issues
**The current version of the code only works with GenePattern 3.9.3 and up!**
Users using the GenePattern Notebook with an older version of GenePattern (3.9.3 or 3.9.4) may
need to log into the GenePattern UI before making use of the notebook. The server status
message and child jobs will also be unavailable. If you are using one of these older versions,
we recommend that you upgrade to the latest version of GenePattern.
# Code of Conduct
We are dedicated to providing a harassment-free experience for all members of the GenePattern community, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form. This code of conduct applies to all GenePattern spaces, including the Google Group, our Git repositories, and our social media accounts, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the GenePattern team.
For more details, see our [Code of Conduct](https://github.com/genepattern/genepattern-notebook/blob/master/Code_of_Conduct.md).
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They are a core \ncomponent of the [g2nb](https://github.com/g2nb) project.\n\n> ### **Looking for classic Jupyter Notebook support?**\n> **Jupyter Notebook support in is available, albeit no longer in active development. You can \n> find it in its own branch. [Just click here!](https://github.com/genepattern/genepattern-notebook/tree/notebook)**\n\n\n### **Prerequisites**\n\n* JupyterLab >= 3.0.0\n* ipywidgets >= 7.0.0\n\n# Docker\n\nA Docker image with nbtools and the full JupyterLab stack is available through DockerHub.\n\n```bash\ndocker pull genepattern/lab\ndocker run --rm -p 8888:8888 genepattern/lab\n```\n\n# Installation\n\nFull installation instructions for casual use are detailed on the \n[GenePattern Notebook website](http://www.genepattern-notebook.org/install/). Users should \nalso consider the [g2nb Notebook Repository](https://notebook.genepattern.org), which \nprovides an install-free cloud deployment of the full suite of g2nb tools, including GenePattern Notebook.\n\n## Development Install\n\nThe installation instructions below are intended for developers who want to install the \nproject from PIP or GitHub for the purposes of software development.\n\n### Install Python\n\nIn order to get the GenePattern Notebook working you will first need to install a compatible \nversion of Python. This means you will need Python 3.6+. We recommend using the \n[Anaconda](https://www.anaconda.com/download/#macos) Python distribution. This is \na scientific version of Python that ships with many of the most popular Python packages for \nscience, math and data analysis (ex: NumPy, SciPy, Pandas, Matplotlib, IPython, etc.).\n\n**Note for Mac Users:** Mac comes with Python, but if you have an older version of the OS \nyou will need to install a newer version, as many older versions of MacOS ship with Python 2.\n\n### Install GenePattern Notebook from GitHub\n\nCopy the contents of genepattern-notebook/extension to your development computer and ensure \nthat the resulting directory if on your Python path. To test this, open Python and try to \n*import genepattern*. If this is successful, you have a copy of the extension available.\n\nIf you don't already have Jupyter installed, you can install it from PIP by running:\n\n> pip install jupyter\n\nFrom here go to the \"Load the GenePattern extension\" step below.\n\n### Install GenePattern Notebook from PIP or Conda\n\nThe easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by \nexecuting one of the following commands:\n\n```bash\npip install genepattern-notebook\n```\n\n*or*\n\n```bash\nconda install -c genepattern genepattern-notebook\n```\n\n### Load the nbtools extension\n\n```bash\n# Install ipywidgets, if you haven't already\njupyter nbextension enable --py widgetsnbextension\njupyter labextension install @jupyter-widgets/jupyterlab-manager\n\n# Clone the nbtools repository\ngit clone https://github.com/genepattern/nbtools-lab-prototype.git\ncd nbtools-lab-prototype\n\n# Install the nbtools JupyterLab prototype\npip install .\njupyter labextension install .\njupyter nbextension install --py nbtools --sys-prefix\njupyter nbextension enable --py nbtools --sys-prefix\n```\n\n### Launch Jupyter\n\nFinally, you may launch JupyterLab by issuing the following command at the terminal:\n\n> jupyter lab\n\nThis will start up the notebook kernel and launch your web browser pointing to the Notebook.\n\n# Related Repositories\n\nThe following GitHub repositories contain code or other data related to the GenePattern \nNotebook environment.\n\n* [g2nb](https://github.com/g2nb/g2nb): A meta-package which installs all of the g2nb tools and extensions.\n* [genepattern-python](https://github.com/genepattern/genepattern-python): The GenePattern \n Library allows for programmatic access to GenePattern from Python, and is used by \n GenePattern Notebook behind the scenes.\n* [nbtools](https://github.com/g2nb/nbtools): The Notebook Tool Manager \n is a tool-agnostic interface and registry for searching, browsing and launching available \n notebook tools in a Jupyter environment.\n* [jupyter-wysiwyg](https://github.com/g2nb/jupyter-wysiwyg): A WYSIWYG editor for \n markdown cells.\n* [example-notebooks](https://github.com/g2nb/example-notebooks): A repository of example notebooks that \n demonstrate functionality or analysis techniques in the GenePattern Notebook environment.\n* [workspace](https://github.com/g2nb/workspace): Scripts, services \n and other infrastructure used in the operation of the GenePattern Notebook Repository.\n\n# Known Issues\n\n**The current version of the code only works with GenePattern 3.9.3 and up!**\n\nUsers using the GenePattern Notebook with an older version of GenePattern (3.9.3 or 3.9.4) may\nneed to log into the GenePattern UI before making use of the notebook. 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