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Requirements and Installation

Requirements

Software

  • Python 2.7.10+
  • pyenv
  • pyenv virtualenv
  • pip

Python Modules

  • h5py
  • NumPy
  • Flask
  • Flask-Restful
  • json
  • pytest
  • Waitress
  • Sphinx
  • sphinx-autobuild

Installation

Basics

Directly from GitHub:

git clone https://github.com/Multiscale-Genomics/mg-rest-adjacency.git
cd mg-rest-adjacency/
pip install -e .
pip install -r requirements.txt

Using pip:

pip install git+https://github.com/Multiscale-Genomics/mg-rest-adjacency.git

Setting up a server

git clone https://github.com/Multiscale-Genomics/mg-rest-adjacency.git

cd mg-rest-adjacency
pyenv virtualenv 2.7.12 mg-rest-adjacency
pyenv activate mg-rest-service
pip install git+https://github.com/Multiscale-Genomics/mg-dm-api.git
pip install -e .
pyenv deactivate

Starting the service:

nohup ${PATH_2_PYENV}/versions/2.7.12/envs/mg-rest-adjacency/bin/waitress-serve --listen=127.0.0.1:5002 rest.app:app &

Testing

Test scripts are located in the test/ directory. Run pytest to from the root repository directory to ensure that the API is working correctly.

The scripts require a valid hdf5 file generated using the scripts from mg-storage-hdf5 and a matching datasets.json file located in the rest/ directory

Documentation

To build the documentation:

pip install Sphinx
pip install sphinx-autobuild
cd docs
make html