LMS RStudio Docker Images

Versioned Dockerfile for the RStudio image used at the MRC LMS, fusing rocker/rstudio with bioconductor/bioconductor_docker, alongside a few extras.

To provide some extra initial functionality, the renv, devtools, rmarkdown, and tidyverse R packages are pre-installed.

Building

Clone and/or checkout the relevant GitHub branch and build locally using docker:

# From scratch
#   git clone git@github.com:LMSBioinformatics/rstudio_image.git && cd rstudio_image
# From an existing clone
#   git pull --all --tags --prune

BRANCH=4.4.0

git checkout $BRANCH
docker build -t lmsbio/rstudio:$BRANCH .

Deploying

Images uploaded to dockerhub can be converted using singularity:

BRANCH=4.4.0

module load singularityce
singularity pull docker://lmsbio/rstudio:$BRANCH

Updating

Dockerfiles for updated versions of R should be within ew named branches. Updates to existing versions should be tagged appropriately.

BRANCH=4.4.0
TAG=$BRANCH_1.0

# create a new branch ...
git checkout -b $BRANCH
# ... or checkout an existing branch
git checkout $BRANCH

# updates ...

# tag and push
git add -A
git commit -m <message>
git tag $TAG
git push --atomic origin $BRANCH $TAG