achubaty/r-spatial-base repository overview

⁠rocker-files

Dockerfiles based on the rocker⁠ project by @eddelbuettel and @cboettig.

All of the images below are available from Docker Hub⁠ and can be pulled using:

docker pull achubaty/<image-name>:<tag>

⁠Package development and testing

The following tags are supported, which correspond to the major.minor R version used in the image:

• latest (uses R 4.5.3)
• 4.4 (uses R 4.4.3)
• 4.3 (uses R 4.3.3)
• 4.2 (uses R 4.2.3)
• 4.1 (uses R 4.1.3)
• 4.0 (uses R 4.0.5)

⁠Usage example

1. launch an instance of a container

docker run --rm -ti -e PASSWORD=yourpassword -p 8080:8787 achubaty/r-spatial-base:4.2

1. connect to the running container's Rstudio instance

Open your web browser and connect to localhost:8080, using username rstudio and the password you set in step 1 above.

⁠SpaDES projects

Generic Dockerfiles for building projects pinned to a specific version of R can be found in dockerfiles/.

• spades-project_4.2.3 builds a generic image for R 4.2.3
• spades-project_4.3.2 builds a generic image for R 4.3.2

These generic dockerfiles are intended to be used to build project-specific images.

⁠Building the base spades-project image

docker build . \
  -f ${HOME}/GitHub/rocker-files/dockerfiles/spades-project_4.3.2.Dockerfile \
  -t achubaty/spades-project:4.3.2

The following tags are supported, which correspond to the major/minor R version used in the image:

• latest (uses R 4.5.3)
• 4.5.0 (uses R 4.5.0)
• 4.4.3 (uses R 4.4.3)
• 4.4.1 (uses R 4.4.1)
• 4.4.0 (uses R 4.4.0)
• 4.3.3 (uses R 4.3.3)
• 4.3.2 (uses R 4.3.2)
• 4.3.1 (uses R 4.3.1)
• 4.2.3 (uses R 4.2.3)

⁠Extending spades-project images

These images can be further extended to produce project-specific images with more advanced configuration options.

⁠Example: LandWeb project

Latest Dockerfile: https://github.com/PredictiveEcology/LandWeb/blob/development/docker/LandWeb-standalone.Dockerfile⁠

To clone specific project repositories from GitHub into the image we added:

• GH_ORG and GH_REPO to specify the GitHub organization (or user) and repository from which the project will be pulled into the image;
• GH_TAG specifies the git branch or tag to checkout;

Additionally, the following optional arguments can be specified:

• USERNAME specifies a specific username (default: rstudio);

When launching an instance of the container:

• a custom PASSWORD can be specified and local input and output directories can be mounted;
• USERID and GROUPID specify the user and group ids, respectively, and can be specified to ensure user permissions of the container match those of the mounted volume (defaults: 1000) (see https://rocker-project.org/images/versioned/rstudio.html#userid-and-groupid⁠);

⁠Usage

1. build the LandWeb-standalone image

cd ~/GitHub/LandWeb

eval `ssh-agent -s`
ssh-add ~/.ssh/id_ed25519_GitHub ## use your ssh key

docker build . \
  --ssh default \
  --build-arg GH_ORG=PredictiveEcology \
  --build-arg GH_REPO=LandWeb \
  --build-arg GH_TAG=development \
  -f docker/LandWeb-standalone.Dockerfile \
  -t achubaty/landweb-standalone:development

1. launch an instance of the container:

RENV_PATHS_CACHE_CONTAINER=/renv/cache
RENV_PATHS_CACHE_HOST=/mnt/shared_cache/renv/cache

docker run -d -it \
  -e USERID=$(id -u) \
  -e GROUPID=$(id -g) \
  -e GITHUB_PAT=$(cat ${HOME}/.Renviron | grep GITHUB_PAT | cut -d '=' -f 2) \
  -e PASSWORD='MySecretPassword' \
  -e RENV_PATHS_CACHE=$RENV_PATHS_CACHE_CONTAINER \
  -v $RENV_PATHS_CACHE_HOST:$RENV_PATHS_CACHE_CONTAINER \
  --memory=128g \
  --cpus=32 \
  -p 127.0.0.1:8080:8787 \
  --mount type=bind,source=/mnt/projects/HRV/LandWeb/inputs,target=/home/rstudio/GitHub/LandWeb/inputs \
  --mount type=bind,source=/mnt/projects/HRV/LandWeb/outputs,target=/home/rstudio/GitHub/LandWeb/outputs \
  --name landweb01 \
  achubaty/landweb-standalone:development

1. connect to the running container's Rstudio instance

Open your web browser and connect to localhost:8080, using username rstudio and the password you set in step 2 above.