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Installing and Using KGTK with Docker

Installing Docker

If you do not have Docker installed, follow the directions at:

https://docs.docker.com/get-docker/

Installing KGTK from the Docker Hub

Pull the latest KGTK image with this command:

docker pull uscisii2/kgtk:latest

Run KGTK on a Docker Command Line

To run KGTK in the command line type (note that if you built the image yourself, you should replace uscisii2/kgtk:latest by kgtk-local in this and the following commands):

docker run -it --rm  --user root -e NB_GID=100 -e GEN_CERT=yes -e GRANT_SUDO=yes uscisii2/kgtk:latest /bin/bash

Accessing Local Data with the Docker Command Line

If you want to load data from your local machine, you will need to mount a volume. For example, to mount the current directory ($PWD) and launch KGTK in command line mode:

docker run -it --rm -v $PWD:/out --user root -e NB_GID=100 -e GEN_CERT=yes -e GRANT_SUDO=yes uscisii2/kgtk:latest /bin/bash

Runnning KGTK in a Jupyter Notebook using Docker

If you want to run KGTK in a Jupyter notebook, mounting the current directory ($PWD) as a folder called /out then you will have to type:

docker run -it -v $PWD:/out -p 8888:8888 uscisii2/kgtk:latest /bin/bash -c "jupyter notebook --ip='*' --port=8888 --no-browser"

You will see a message similar to:

[C 22:36:40.418 NotebookApp]

    To access the notebook, open this file in a browser:
        file:///root/.local/share/jupyter/runtime/nbserver-1-open.html
    Or copy and paste one of these URLs:
        http://092260f3740e:8888/?token=83945df95e9b1f5f7594597d3925960fc89dbefaed4ada7d
     or http://127.0.0.1:8888/?token=83945df95e9b1f5f7594597d3925960fc89dbefaed4ada7d

Copy the localhost URL (in the case above http://127.0.0.1:8888/?token=83945df95e9b1f5f7594597d3925960fc89dbefaed4ada7d, this is random every time) and paste it in your browser. In order to run KGTK commands in a notebook, remember to add %%bash in the line before your command, as shown below:

%%bash
kgtk --help

As a result, now you should be able to see a help message similar to the one depicted below:

Diagram

!!! note if you want to load data from your local machine or save the results obtained with KGTK, you will need to mount a volume as described above. Notebooks stored inside the container will be erased after the container finishes its execution.

!!! note Older versions of KGTK (0.3.2 and 0.2.1) require --allow-root as part of the jupyter notebook command jupyter notebook --ip='*' --port=8888 --allow-root --no-browser

Additional Docker Images

More information about all available versions and tags is available here: https://hub.docker.com/repository/docker/uscisii2/kgtk. For example, the dev branch is available at uscisii2/kgtk:latest-dev.

Building a Docker Image

You can build a local Docker image after installing KGTK from GitHub. Use the following commands starting from your KGTK installation folder:

cd docker/
docker build -t kgtk-local .

Updating your KGTK installation

To update your version of KGTK, then just pull the most recent image:

docker pull <image_name>]

where <image_name> is the tag of the image of interest (e.g. uscisii2/kgtk:latest)