2. Installation

The following instructions describe how to install datanator onto Ubuntu Linux 16.04. Datanator only supports Python 3.

2.1. Install dependencies

First, please install the following dependencies:

The following shell commands can be used to install these dependencies onto Ubuntu Linux 16.04:

apt-get install \
    git \
    libcairo2-dev \
    libeigen3-dev \
    libxml2-dev \
    python \
    python-pip \
    swig \

cd /tmp
wget https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/openbabel-2.4.1.tar.gz/download -O /tmp/openbabel-2.4.1.tar.gz
tar -xvvf /tmp/openbabel-2.4.1.tar.gz
cd openbabel-2.4.1
mkdir build
cd build
cmake ..
make install

2.2. Install datanator

Second, please run the following shell commands to clone and install datanator from GitHub:

git clone git@github.com:KarrLab/datanator.git
python3 -m pip install -e datanator

Because datanator is under active development, we recommend regularly pulling the latest revision of datanator from GitHub.

2.3. Run datanator

The API for datanator can be run with a test and production server.

In order to run the test server, run the following command:

python3 manage.py runserver

NOTE: You will need to have the correct configuration in the datanator/__init__.py file. Configurations can be found in datanator/config.py include:

  • LocalDevelopmentConfig - Local server for database
  • CircleTestingConfig - CircleCI server for database
  • BuildConfig - Docker Compose/UCONN HPC server for database
  • ProductionConfig - AWS RDS server for database (PRIVATE)

In order to run the production server, run the following command:

gunicorn -w 4 -b localhost:5000 --timeout 120 manage:app

This command will create a gunicorn production server with 4 workers at the localhost:5000 address with a timeout of 2 min

Contact Saahith for any questions regarding installation and running the server