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BCaPE Shiny app

Web application for the Breast Cancer PDTX Encyclopaedia built using the R Shiny framework.

The data for the Shiny app are contained in an SQLite database file named bcape.sqlite. The SQLite database within this folder is empty but contains the schema definitions for all tables and indexes. See the processing folder for details on how to populate the database.

R package dependencies

The application depends on the following R packages which can be installed using the R install.packages function.

Running the application standalone

To run the Shiny app standalone:

Rscript start_shiny_app.R

The application should be launched in a new browser window.

Deployment within Shiny Server

Alternatively, to run within Shiny Server, copy the R code (files ending with '.R'), the database (bcape.sqlite), the analytics JavaScript function (analytics.js) and the images within the www subdirectory to a new directory named bcape within the Shiny server site directory, usually /srv/shiny-server. The application should be available at http://host:port/bcape, where host and port need to be substituted with the name of the host on which Shiny Server is running and the port number on which it is configured to listen (see /etc/shiny-server/shiny-server.conf).

Deployment using Docker

This folder contains a Dockerfile used to build a Docker image in which Shiny Server, R, the BCaPE web application and all its R package dependencies are installed. The Docker image is built on the shiny-base image which packages Shiny Server, R and the tidyverse R packages.

The Docker image is available on Docker Hub and can be retrieved as follows:

docker pull crukcibioinformatics/bcape

To deploy the application within a Docker container running Shiny Server:

chmod ugo+r bcape.sqlite
mkdir -p logs
chmod ugo+rwx logs
docker run -u shiny -d -p 3838:3838 \
  -v ${PWD}/bcape.sqlite:/srv/shiny-server/bcape/bcape.sqlite \
  -v ${PWD}/logs:/var/log/shiny-server \
  crukcibioinformatics/bcape

Note that this replaces the empty database contained within the Docker image with the bcape.sqlite file in the current directory on the host file system. Likewise, a log directory is created and bound into the container so that logging information is accessible outside the container.

Similarly we could replace the Shiny Server configuration to change some configuration settings by mounting an external configuration file as /etc/shiny-server/shiny-server.conf within the container. See the shiny-base Docker image for more details on how to configure Shiny Server in this way.

The application should be accessible at http://localhost:3838/bcape.

By default Shiny Server listens on port 3838. This can be remapped to another port using Docker with the -p option.

Deployment using Singularity

The BCaPE site is deployed using Singularity, which is another container system. A Singularity image, in which Shiny Server, R, the BCaPE Shiny application and its R package dependencies are installed, can be built from the Docker image available on Docker Hub as follows:

singularity build bcape.sif docker://crukcibioinformatics/bcape

This does not require Docker to be installed.

The image can be run as follows:

mkdir -p logs
singularity run \
  -B bcape.sqlite:/srv/shiny-server/bcape/bcape.sqlite \
  -B logs:/var/log/shiny-server \
  bcape.sif

Google analytics

Usage of the application can be monitored using Google Analytics. For this an account on Google Analytics will need to be set up and a tracking ID obtained.

The following JavaScript function should be added to analytics.js:

(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
  })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');

  ga('create', 'UA-12345678-1', 'auto');
  ga('send', 'pageview');

  $(document).on('shiny:value', function(event) {
    ga('send', 'event', 'update', event.name);
  });

where the tracking ID UA-12345678-1 should be substituted with the one to be used for the deployed application.

If deploying with Docker, analytics.js can be mounted within the container as follows:

docker run -u shiny -d -p 3838:3838 \
  -v ${PWD}/bcape.sqlite:/srv/shiny-server/bcape/bcape.sqlite \
  -v ${PWD}/analytics.js:/srv/shiny-server/bcape/analytics.js \
  -v ${PWD}/logs:/var/log/shiny-server \
  crukcibioinformatics/bcape

Similarly with Singularity:

singularity run \
  -B bcape.sqlite:/srv/shiny-server/bcape/bcape.sqlite \
  -B analytics.js:/srv/shiny-server/bcape/analytics.js \
  -B logs:/var/log/shiny-server \
  bcape.sif