Installing

cockatoo is in the Python Package Index.

Installing with Conda

First download and installed either Anaconda or Miniconda.

Create a new conda environment, checkout the cockatoo source code, and install the dependencies:

$ conda create -c keiserlab -c rdkit -c sdaxen --name cockatoo-dev e3fp
$ conda activate cockatoo-dev

# Note on Linux may want to install ncurses if using Miniconda
$ conda install -c default ncurses

$ git clone git://github.com/ubccr/cockatoo.git cockatoo
$ cd cockatoo
$ pip install -e .

Installing with pip

To install cockatoo via pip:

$ pip install cockatoo

Requirements

cockatoo requires e3fp, RDKit and marshmallow:

# Note e3fp requires RDKit
$ pip install e3fp
$ pip install marshmallow

cockatoo’s command line tool requires click:

$ pip install Click

The hierarchical clustering module requires python packages: numpy,scipy,matplotlib,brewer2mpl:

$ pip install numpy
$ pip install scipy
$ pip install brewer2mpl

Installing from source

To install cockatoo from source checkout the latest code from github:

$ git clone git://github.com/ubccr/cockatoo.git cockatoo
$ cd cockatoo
$ python setup.py install