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.

To install, first install the Anaconda Python Distribution, which comes pre-packaged with a bunch of the scientific packages we use all the time, pre-installed.

Create a flotilla sandbox

We recommend creating a “sandbox” where you can install any and all packages without disturbing the rest of the Python distribution. This way, your flotilla environment is completely insulated from everything else, just in case something goes wrong with You can do this with

conda create --yes flotilla_env pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml

You’ve now just created a “virtual environment” called flotilla_env (the first argument). Now activate that environment with,

source activate flotilla_env

Now at the beginning of your terminal prompt, you should see:

(flotilla_env)

Which indicates that you are now in the flotilla_env virtual environment. Now that you’re in the environment, follow along with the non-sandbox installation instructions.

Install and update all packages in your environment

To make sure you have the latest packages, on the command line in your terminal, enter this command:

conda update --yes pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml

Not all packages are available using conda, so we’ll install the rest using pip, which is a Python package installer and installs from PyPI, the Python Package Index.

pip install seaborn fastcluster brewer2mpl pymongo gspread husl semantic_version joblib

Next, to install the latest release of flotilla, do

pip install flotilla

If you want the bleeding-edge master version because you’re a developer or a super-user, (we work really hard to make sure it’s always working but could be buggy!), then install the git master with,

pip install git+git://github.com/yeolab/flotilla.git

Old OSX Installation instructions

This part only needs to be done once

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 --yes 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 --yes -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.

Docker 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.

Here are instructions to get an active docker image. These instructions have not been tested on Windows or Linux.

Note: On Mac OS X and Windows you will need to start docker through the “boot2docker” application before you can use docker.

  1. Install docker ( ≥ version 1.3) according to the instructions appropriate for your system.

  2. Then start flotilla on the command line (OS X Terminal application):

    curl https://raw.githubusercontent.com/YeoLab/flotilla/master/docker/start_docker.py | python

After the ipython notebook interface opens, test the installation with our test dataset by running the following commands in a new notebook:

import flotilla study = flotilla.embark(“http://sauron.ucsd.edu/flotilla_projects/neural_diff_chr22/datapackage.json”) study.interactive_pca()
Olga B. Botvinnik is funded by the NDSEG fellowship and is a NumFOCUS John Hunter Technology Fellow.
Michael T. Lovci was partially funded by a fellowship from Genentech.
Partially funded by NIH grants NS075449 and HG004659 and CIRM grants RB4-06045 and TR3-05676 to Gene Yeo.