princessmaximacenter/gi-analysis repository overview

⁠ReportGICandidates tool

An R-shiny tool that aids in viewing candidate genetic interactions in childhood cancer.

For reproducibility and ease of deployment a docker image exists.

⁠How to build

Have docker installed, be in the current directory and run:

docker build --tag gi-analysis:latest .

⁠How to run

Have docker installed and run it as follows:

docker run -p 3838:3838 gi-anlaysis:latest

Use your browser of choice to visit http://localhost:3838⁠

⁠How to develop

The image can be build once and be fully self contained. However, rebuilding the image every time you make a change is a bit of a hassle.

After you have build the image, and for development purposes you can run it as follows:

docker run \
  --rm -it \
  --volume $(pwd)/data:/srv/shiny-server/data \
  --volume $(pwd)/www:/srv/shiny-server/www \
  --volume $(pwd)/app.R:/srv/shiny-server/app.R \
  -p 3838:3838 \
  gi-analysis:latest
  

This will start a container that will automagicly update if the app.R is changed.

⁠Deploy/share a new version

Docker has online repositories to contain images. Best practice is to upload it to docker hub and load it via a pull to any servers you want to use it for hosting.

Retag your latest build having tagname the version you want to upload

docker tag \
  gi-analysis:latest \
  princessmaximacenter/gi-analysis:tagname

Push the image to docker hub:

docker push princessmaximacenter/gi-analysis:tagname