Install Guide

This guide is a resource for using the Allen SDK package. It is maintained by the Allen Institute for Brain Science.

The Allen SDK was developed and tested with Python 2.7.13 and Python 3.6.4, installed as part of Anaconda Python distribution version 4.3.13. We do not guarantee consistent behavior with other Python versions.

Quick Start Using Pip

First ensure you have pip installed. It is included with the Anaconda distribution.

pip install allensdk

To uninstall the SDK:

pip uninstall allensdk

Other Distribution Formats

The Allen SDK is also available from the Github source repository.

Required Dependencies

• NumPy
• SciPy
• matplotlib
• h5py
• pandas
• pynrrd
• Jinja2

Optional Dependencies

• pytest
• coverage

Installation with Docker (Optional)

Docker is an open-source technology for building and deploying applications with a consistent environment including required dependencies. The AllenSDK is not distributed as a Docker image, but example Dockerfiles are available.

1. Ensure you have Docker installed.

2. Use Docker to build one of the images.

   Anaconda:

   docker pull alleninstitute/allensdk
   

   Other docker configurations are also available under docker directory in the source repository.

3. Run the docker image:

   docker run -i -t -p 8888:8888 -v /data:/data alleninstitute/allensdk /bin/bash
   cd allensdk
   make test
   

4. Start a Jupyter Notebook:

   cd allensdk/doc_template/examples_root/examples/nb
   jupyter-notebook --ip=* --no-browser