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Gene_Catalog_Rshiny

BAltic Gene Set - BAGS.v1.1

Deploying to the Serve plattform

Configuration

The application is configured in the .Renviron.template file. This is initially configured for deployment to the Serve plattform.

Setup

Upload the dataset to Serve and extract such that the contents reside directly under project-vol. The project-vol directory will be mapped to /data in the container.

Create as custom app type in Serve with the following values:

  • Persistent Volume: project-vol
  • Path: /data
  • Port: 3838
  • Image: specify the path to the published image
  • User ID: 999

Viewing logs

cat /rlogs/app.log

ls /var/log/shiny-server

Local deployments

Build and run a docker image locally

Configure for the local environment in the .Renviron.template file

R_LOGLEVEL = "DEBUG"
R_LOGFILE = "../rlogs/app.log"
DATA_DIR = "../data"

Build the docker image

docker build -t gene-catalog-rshiny:dev .

Run the container without data folder

docker run -p 127.0.0.1:3838:3838 gene-catalog-rshiny:dev

Or, run the container with a mounted local data folder

APP_PATH="PATH-TO-GIT-REPO/Gene_Catalog_Rshiny"

docker run -p 127.0.0.1:3838:3838 \
-v $APP_PATH/data:/data \
--memory=16g --memory-swap=20g \
gene-catalog-rshiny:dev

Browse to the app at http://localhost:3838/

Local development

If planning to run in local environment from R terminal: Copy and edit the .Renviron file

cp ./.Renviron.template ./app/.Renviron

If using a local data directory, create the directory and copy a data file there named existing.csv. This can be used for diagnosing permission problems.

mkdir data