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Docker Installation Instructions

Docker is the preferred method to obtain the most up-to-date version of flotilla. Every change we make to the source code triggers a new build of a virtual machine that contains flotilla and all its dependencies.

Please follow instructions here to get, install, and run the flotilla image.

OS X Installation instructions

The following steps have been tested on a clean install of Mavericks 10.9.4.

All others must fend for themselves to install matplotlib, scipy and their third-party dependencies.

This part only needs to be done once

  • Install anaconda

  • Install Xcode (this can take an hour)

  • Open Xcode and agree to terms and services (it is very important to read them thoroughly)

  • Install homebrew

    ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

  • Install freetype:

    brew install freetype

  • Install heavy packages (this can take an hour or more)

conda install pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml`
  • Create a virtual environment
conda create -n flotilla_env pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml`

  • Switch to virtual environment

    source activate flotilla_env

  • Install flotilla and its dependencies (this can take a few minutes):

    pip install git+https://github.com/YeoLab/flotilla.git

  • Create a scratch space for your work

    mkdir ~/flotilla_scratch

  • Make a place to store flotilla projects

    mkdir ~/flotilla_projects

  • Go back to the real world

    source deactivate

  • switch to virtual environment

    source activate flotilla_env

  • start an ipython notebook:

    ipython notebook --notebook-dir=~/flotilla_scratch

  • create a new notebook by clicking New Notebook

  • rename your notebook from "Untitled" to something more informative by clicking the title panel.