rocker-ultra

Containerised RStudio with bells+whistles for HPC and everywhere

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rocker-ultra aims to simplify launching an RStudio server in Singularity with a single wrapper script, with managment of package directories per-version in your home directory, auto-free port finding, per-session password generation and SSH port forwarding instructions for free. It is based on the containers developed by the rocker project (but not affiliated).

By default rocker-ultra uses a custom image based on rocker/rstudio but with Seurat dependencies pre-installed.

Quickstart

Run:

# Download the `rstudio.sh` from this repo
wget https://raw.githubusercontent.com/MonashBioinformaticsPlatform/rocker-ultra/main/rstudio.sh

chmod +x ./rstudio.sh
./rstudio.sh

It may take some time to download images. Eventually you'll be presented with instructions to login, including a generated password, eg

INFO:    Creating SIF file...
INFO:    Build complete: rstudio_3.6.0.sif

Finding an available port ...
Got one !

On you local machine, open an SSH tunnel like:
  ssh -N -L 8787:localhost:8787 [email protected]
  or
  ssh -N -L 8787:localhost:8787 [email protected]

Point your web browser at http://localhost:8787

Login to RStudio with:
  username: myusername
  password: Y9qmTCxlM30ArhY7biC5

Protip: You can choose your version of R from any of the tags listed here: https://hub.docker.com/r/rocker/rstudio/tags
        and set the environment variable IMAGE, eg
        IMAGE=rocker/rstudio:3.5.3 rstudio.sh

Starting RStudio Server (R version 3.6.0)

If you'd like to select your R version, set the IMAGE environment variable like this:

IMAGE=rocker/rstudio:3.5.3 ./rstudio.sh

As long as there is a corresponding versioned container provided by Rocker, most common R versions should work.

Note that by default the script uses a custom image based on rocker/rstudio that has the Seurat package and required dependencies pre-installed. You can find available versions under 'Packages' in the sidebar on Github (eg, the rocker-seurat releases).

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On M3 / Massive

Specific instructions for the M3 HPC site are here.

Building a container

You probably don't need to build these containers yourself, since pre-built versions already exist on Dockerhub / Github Pacakges, and are automatically build via CI. However, you may want to build one to generate a custom version for some purpose.

For example:

REGISTRY="pansapiens"
VERSION_TAG="4.2.3-4.3.0"
docker build \
  -t "${REGISTRY}/rocker-seurat:latest" \
  -t "${REGISTRY}/rocker-seurat:${VERSION_TAG}" \
  -f "dockerfiles/rocker-seurat/${VERSION_TAG}/Dockerfile" \
  "dockerfiles/rocker-seurat/${VERSION_TAG}"

# Generate a Singularity image file
singularity build "rocker-seurat_${VERSION_TAG}.sif" "docker-daemon://${REGISTRY}/rocker-seurat:${VERSION_TAG}"

# Run with your custom Singularity image
IMAGE="./rocker-seurat_${VERSION_TAG}.sif" ./rstudio.sh

History

rocker-ultra began with this gist