Platform for integrating genomic analysis with Jupyter Notebooks.
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README.md

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GenePattern Notebook

The GenePattern Notebook 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 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.

Installation

Full installation instructions for casual use are detailed on the GenePattern Notebook website. Users should also consider the GenePattern Notebook Repository, which provides an install-free cloud deployment of the GenePattern Notebook environment.

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 3.4+. We recommend using the Anaconda 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 you will need to install a newer version, as OSX ships 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:

pip install genepattern-notebook

or

conda install -c genepattern genepattern-notebook

Load the GenePattern extension

In Jupyter 5.2 and earlier, before you can use the GenePattern extension for the very first time, you need to enable it by running command lines below.

In Jupyter 5.3 and later this is automatic and there is no need to run these commands.

jupyter nbextension enable --py widgetsnbextension

jupyter nbextension install --py nbtools

jupyter nbextension enable --py nbtools

jupyter nbextension install --py genepattern

jupyter nbextension enable --py genepattern

jupyter serverextension enable --py genepattern

Launch Jupyter

Finally, you may launch Jupyter Notebook by issuing the following command at the terminal:

jupyter notebook

This will start up the notebook kernel and launch your web browser pointing to the Notebook.

Updating GenePattern Notebook

If you want to update GenePattern Notebook to a more recent version on PIP, run the following command:

pip install --upgrade --no-deps genepattern-notebook

Related Repositories

The following GitHub repositories contain code or other data related to the GenePattern Notebook environment.

  • genepattern-python: The GenePattern Library allows for programmatic access to GenePattern from Python, and is used by GenePattern Notebook behind the scenes.
  • nbtool-manager: 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: A WYSIWYG editor for markdown cells.
  • example-notebooks: A repository of example notebooks that demonstrate functionality or analysis techniques in the GenePattern Notebook environment.
  • notebook-docker: A collection of Dockerfiles which are used to build containers encapsulating the GenePattern Notebook environment.
  • notebook-repository: 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.

Feature Support

Most common GenePattern features are supported in the GenePattern Notebook environment. A few, however, have yet to be implemented. GenePattern features that are not yet supported include:

  • Batch job submission
  • GenomeSpace integration