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LMS RStudio Docker Images

Versioned Dockerfile for the RStudio image used at the MRC LMS, building extra compilation compatibility into rocker/rstudio:

  • maths headers: libfftw3-dev, libgsl-dev, libglpk40-dev, libglpk-dev
  • compression headers: liblzma-dev, libbz2-dev, libdeflate-dev
  • compatibility headers: build-essential, libhdf5-dev, libpng-dev, libboost-all-dev, libxml2-dev

The image is also built to include two generic dependencies of RStudio:

  • renv for creating reproducible environments in R
  • rmarkdown to facilitate RStudio's knitting functionality

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

Deployed images uploaded to dockerhub can be converted using singularity:

BRANCH=4.4.0

singularity pull docker://lmsbio/rstudio:$BRANCH

Updating

Image files for updated versions of R should be within a new named branch. 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

# update

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