infrastructure_submodules

Components of the SDAL infrastructure (in submodule form)

Porting submodules from: https://github.com/bi-sdal/dockerimages

Docker Containers

R

rpkgs

Installing package for all users simultaneously

This allows a package to be accessable to all users without separate compilling and installations.

1. Go into the rpkgs container: docker exec -it rpkgs bash
2. Launch R: R
3. Install the package you want for everyone, e.g., install.packages('tidyverse')

Installing package that needs a system library for all users

Some R packages need a system library installed, e.g, geojsonio needs the libjq system library installed. In this example, CENTOS needs the jq-devel library installed.

Install it in container directly

1. Go into the user's container, e.g., docker exec -it rstudio_chend bash
2. Install the system library, e.g., yum install jq-devel
3. Install the package of interest in R, e.g., install.packages('geojsonio')

Installing the system library and R package for everyone

If the above works, you can install the package in the image itself

Installing the system library for all docker images

1. Do this on snowmane, the test server
   1. Add the installation in the mro Dockerfile, e.g., yum install -y jq-devel && \
   2. Build the base mro, rpkgs, rstudio, and shiny images (you can use the dbuild command from the dockerimages setup)
   3. Push the images to dockerhub, docker push

   docker push sdal/mro-c7sd_auth
   docker push sdal/rss-mro-c7sd_auth
   docker push sdal/rpkgs-mro-c7sd_auth
   docker push sdal/shy-mro-c7sd_auth

2. Do this on lightfoot, the production server
   1. Pull the images from dockerhub, docker pull

   docker pull sdal/mro-c7sd_auth
   docker pull sdal/rss-mro-c7sd_auth
   docker pull sdal/rpkgs-mro-c7sd_auth
   docker pull sdal/shy-mro-c7sd_auth

   2. Start up the rstudio containers, docker-compose -f rstudio-compose.yml up -d --no-recreate