INRAE-onto-visualization

Interface for the synthetic visualization of relational data with ontologies (Florilege).

Install a Docker Container

This section suppose that you are able to pull and run docker containers. For more information on Docker, see https://www.docker.com/.

Docker is an open source tool to build, ship, and run distributed applications in an isolated environment.

Please read this section completely to make sure you start the appropriate installation procedure.

Prerequisites

We recommend the following minimal configuration (or above) :

• 2 vCPUs i386, x86_64
• RAM 4Go
• Ubuntu 18.04.5 LTS
• Docker version 19.03.8

Install docker by using this command

sudo apt install docker.io

The ontology files need to be stored in a folder accessible by docker (referenced by /absolute/path/to/data/ below). There are :

• BioNLP-OST+EnovFood-Habitat.obo
• BioNLP-OST+EnovFood-Phenotype.obo
• microorganisms.obo
• Use_V2.obo

Building from source code

1. Build image

sudo docker build -f docker/Dockerfile -t  inrae/onto:latest .

2. Save image

sudo docker save inrae/onto > inrae.tar

And transfer the .tar file to the server

3. Load image and run container

On the server

sudo docker load < inrae.tar
sudo docker run -it -d --rm -v /absolute/path/to/data/:/srv/shiny-server/data -p 80:3838 --name inrae inrae/onto:latest

• /absolute/path/to/data/ must be the path to data folder which contains all .obo files.

It takes a few minutes for the container to start because of the .obo files to load. When ready, you should see the line: Listening on http://0.0.0.0:3838. Then, launch a browser at http://localhost.

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NOTE

To facilitate handling of the previous commands, you can use the scripts build.sh and run.sh for building and starting the docker container. So, run ./build.sh to build image and ./run.sh to run the container.

Please, don't forget to change the path to data folder in the run.sh file.

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Configuration

Labels and parameters are stored in inrae/conf.ini. When changed the docker image needs to be rebuild.

Miscellaneous

If a problem happens, you can check logs by running :

sudo docker logs inrae