Installation on Ubuntu with Conda

0. System Install

sudo apt-get install git

1. Download and install miniconda

See : http://conda.pydata.org/miniconda.html

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x  Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh

2. Create your own virtual environment

conda create --name rhizoscan python


# Activate your virtual environnement each time
source activate rhizoscan

3. Install Rhizoscan dependencies

conda install sphinx jupyter nose coverage anaconda-client
conda install numpy scipy matplotlib scikit-image opencv pil pillow scikit-learn
conda install -c openalea openalea.mtg openalea.vpltk openalea.visualea openalea.core

3.1 Download & install TreeEditor

conda install -c openalea -c openalea/label/unstable openalea.treeeditor

3.2 Download & install RSML-conversion-tools

conda install -c openalea -c openalea/label/unstable rsml

4. Install & test Rhizoscan

git clone https://github.com/openalea-incubator/rhizoscan
cd rhizoscan
python setup.py develop --prefix=$CONDA_PREFIX
nosetests test