READMY.md

Biodiversity Viewer. Module: Web Viewer

This repository provides several use cases for the application.

1. Use the application to work on your local computer;
2. Publish the application using Shiny Server Docker image;
3. Publish the application using Shiny Docker image to run using Shiny proxy.

Use the application to work on your local computer

Application files are located in the app folder.

Shiny Server

Shiny Server Docker image

Build Web Biodiversity Viewer shiny server Docker image

docker build --file ./shiny_server.dockerfile -t biodiversity_viewer_shiny_server .

Run biodiversityviewer docker image

docker run -d --name shinyserver -p 3838:3838 -v "gbif_data:/srv/shiny-server/gbif_data" biodiversity_viewer_shiny_server

or

docker run -d --name shinyserver -p 3838:3838 -v "gbif_data:/srv/shiny-server/gbif_data" antonbiatov/biodiversity_viewer_shiny_server:latest

ShinyProxy

Configure docker

you need to configure host docker https://www.shinyproxy.io/documentation/getting-started/ depende on type of operation system.

For example on Windows:

sc config docker binpath= "C:/Program Files/Docker/Docker/resources/dockerd.exe --run-service -H tcp://127.0.0.1:2375"

Build Shiny Docker image to run in ShinyProxy

docker build --file ./shiny_app.dockerfile -t biodiversity_viewer_shiny_app .

Test run shiny app

docker run --rm -d --name biodiversityviewershinyapp -p 3838:3838 -v "gbif_data:/home/app/gbif_data" biodiversity_viewer_shiny_app

Create shinyproxy network

docker network create shinyproxy-net

Get ShinyProxy

docker build --file ./shinyproxy.dockerfile -t biodiversity_viewer_shinyproxy .

Test run shinyproxy

docker run --rm -it --name shinyproxy -v "//var/run/docker.sock:/var/run/docker.sock" --net shinyproxy-net -p 8080:8080 biodiversity_viewer_shinyproxy

Run SinyProxy

docker run -d -v /var/run/docker.sock:/var/run/docker.sock --net sp-example-net --name shinyproxy -p 8080:8080 biodiversity_viewer_shinyproxy