Installation

Draco-Stem Installation Procedure

Prerequisite : Install Miniconda

• Download the miniconda installer from the official website repo.continuum.io

  • LINUX: https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

  • MAC: https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh

  • Windows: https://repo.continuum.io/miniconda/Miniconda2-latest-Windows-x86_64.exe

  You can also use wget to perform this download from a shell (LINUX or MAC):

  • LINUX: wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

• Install miniconda by running the installer:

  • LINUX: Open a new terminal window, go to the directory where you downloaded the installer and run:

    bash Miniconda2-latest-Linux-x86_64.sh
    rm Miniconda2-latest-Linux-x86_64.sh
    

  • MAC: Open a new terminal window, go to the directory where you downloaded the installer and run:

    bash Miniconda2-latest-MacOSX-x86_64.sh
    rm Miniconda2-latest-MacOSX-x86_64.sh
    

  • Windows: Execute the installer and follow the instructions

  During the installation you will be asked a number of choices

  • You can set up the directory of your choice when asked, e.g. ~/.miniconda

  • Make sure to answer YES when asked to add conda to your PATH

• You should now have miniconda properly installed; test your installation by running conda in a terminal to make sure the command is found

Conda tips:

• Get out of the current conda environment : source deactivate
• View the available environments : conda env list

User procedure

• Create a new conda environment where to install TissueLab (named tissuelab-env for instance)

conda create -n tissuelab-env -y python=2.7

• Activate the environment

source activate tissuelab-env

• Install TissueLab and its dependencies from the tissuelab channel:

conda install -c tissuelab tissuelab.tissuelab

• Download the Draco-Stem sources to the directory of your choice and install them

git clone https://github.com/VirtualPlants/tissue_analysis.git
cd tissue_analysis
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/VirtualPlants/draco_stem.git
cd draco_stem
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

Developer procedure

• Install git

• Create a file called tissuelab.yml containing the list of dependencies

name: tissuelab
channels:
  - openalea
  - defaults
dependencies:
  - python=2.7
  - ipython-qtconsole=3.2.1
  - jinja2
  - numpy
  - scipy=0.16
  - matplotlib=1.5.1
  - pandas
  - pillow
  - vtk=5.10
  - nose
  - openalea.sconsx
  - pip:
      - pyqode.python

• Define a new conda environment

conda env create -f tissuelab.yml

• Activate the environment

source activate tissuelab

• Download the OpenAlea sources and TissueLab packages to the directory of your choice and install them

You may have to do export PREFIX=$CONDA_ENV_PATH

git clone https://github.com/openalea/openalea.git
cd openalea
git checkout develop
python multisetup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/openalea/openalea-components.git
cd openalea-components
git checkout develop
python multisetup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/VirtualPlants/cellcomplex.git
cd cellcomplex
git checkout develop
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/VirtualPlants/tissue_analysis.git
cd tissue_analysis
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/VirtualPlants/tissuelab.git
cd tissuelab
git checkout develop
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

git clone https://github.com/VirtualPlants/draco_stem.git
cd draco_stem
python setup.py develop --prefix=$CONDA_ENV_PATH
cd ..

Testing

• Check your installation by going in the test directory of the Draco-Stem package and running nosetests:

conda install nose
cd draco_stem/test
nosetests -v