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 \
zlib1g-dev
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
make install
ldconfig
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
pip3 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