2. Installation

The following instructions describe how to install datanator onto a Debian-based Linux OS using the docker image wc_env <https://hub.docker.com/r/karrlab/wc_env>

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 update

apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    gnupg-agent \

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

sudo add-apt-repository \
    "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
    $(lsb_release -cs) \

sudo apt-get update

sudo apt-get install docker-ce docker-ce-cli containerd.io

sudo curl -L "https://github.com/docker/compose/releases/download/1.26.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose

sudo chmod +x /usr/local/bin/docker-compose

sudo ln -s /usr/local/bin/docker-compose /usr/bin/docker-compose

2.2. Install datanator

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

mkdir karr_lab
mkdir ~/.wc
cd ./karr_lab
git clone git@github.com:KarrLab/pkg_utils.git
git clone git@github.com:KarrLab/wc_utils.git
git clone git@github.com:KarrLab/karr_lab_aws_manager.git
git clone git@github.com:KarrLab/datanator_query_python.git
git clone git@github.com:KarrLab/datanator.git
cd ./datanator
nano docker-compose.yml # change ``zl`` on line 13 to the proper username. Save and exit by pressing ``Ctrl + X`` followed by ``Y``
docker-compose up -d

2.3. Run datanator

One needs to find the docker container ID in order to use Datanator package:

docker ps
docker exec -it <container_id> bash
cd karr_lab/datanator

All python scripts in datanator dicrectory can be run with python3, for example:

python3 datanator/data_source/corum_nosql.py

Running the command above will parse Corum <http://mips.helmholtz-muenchen.de/corum/> and store the parsed data in KarrLab’s MongoDB.

Contact Yang for any questions regarding installation and running the package.