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Bioconductor on Apollo

This repository provides a Dockerfile that extends the official Bioconductor Docker image by adding some packages including the HPC job scheduler SLURM. GitHub actions build the image and push it to GitHub Packages.

Additionally supported packages

Bioconductor Docker containers are based on Rocker project images, which provide RStudio Server, a full featured IDE via a web browser. To the Rocker project's images, the Bioconductor developers add all the system dependencies required to support Bioconductor R libraries. We extend the container further by adding:

ML libraries for transformers and convolutional neural networks
System dependencies to support bedr, ctrdata, monocle3, fnmate and datapasta
genomics tools like sra-tools, bcftools and bedops
DNAnexus support (DX toolkit, dxfuse)
SLURM
JupyterLab
VSCode LiveShare, R devcontainer dependencies, miniconda

Bioconductor version 3.19

Apollo

Build the container image for the HPC:

module load singularity
singularity pull -F /opt/singularity-images/rbioc/vscode-rbioc_3.19.sif docker://ghcr.io/drejom/vscode-rbioc:v2024-7-17

And launch on the HPC:

sbatch /opt/singularity-images/rbioc/rbioc319.job

Gemini

Build the container image for the HPC:

module load singularity
singularity pull -F /packages/singularity/shared_cache/rbioc/vscode-rbioc_3.19.sif docker://ghcr.io/drejom/vscode-rbioc:v2024-7-17

And launch on the HPC:

# RStudio not supported on Gemini
#sbatch /packages/singularity/shared_cache/rbioc/rbioc319.job
# Use vscode tunnels

Bioconductor version 3.18

Apollo

Build the container image for the HPC:

module load singularity
singularity pull -F /opt/singularity-images/rbioc/vscode-rbioc_3.18.sif docker://ghcr.io/drejom/vscode-rbioc:v2023-11-27

And launch on the HPC:

sbatch /opt/singularity-images/rbioc/rbioc318.job

Gemini

Build the container image for the HPC:

module load singularity
singularity pull -F /packages/singularity/shared_cache/rbioc/vscode-rbioc_3.18.sif docker://ghcr.io/drejom/vscode-rbioc:v2023-11-27

And launch on the HPC:

#sbatch /packages/singularity/shared_cache/rbioc/rbioc318.job

Bioconductor version 3.17

Apollo

Build the container image for the HPC:

module load singularity
singularity pull -F /opt/singularity-images/rbioc/vscode-rbioc_3.17.sif docker://ghcr.io/drejom/vscode-rbioc:v2023-9-26

And launch on the HPC:

sbatch /opt/singularity-images/rbioc/rbioc317.job

Gemini

Build the container image for the HPC:

singularity pull -F /packages/singularity/shared_cache/rbioc/vscode-rbioc_3.17.sif docker://ghcr.io/drejom/vscode-rbioc:v2023-10-24

And launch on the HPC:

#sbatch /opt/singularity-images/rbioc/rbioc317.job

Bioconductor version 3.16

Build the container for the HPC:

module load singularity
singularity pull -F /opt/singularity-images/rbioc/vscode-rbioc_3.16.sif docker://ghcr.io/drejom/vscode-rbioc:v2023-1-8

And launch on the HPC:

sbatch /opt/singularity-images/rbioc/rbioc316.job

Bioconductor version 3.15

Build the container for the HPC:

module load singularity
singularity pull -F /opt/singularity-images/rbioc/vscode-rbioc_3.15.sif docker://ghcr.io/drejom/vscode-rbioc:v2022-10-14

And launch on the HPC:

sbatch /opt/singularity-images/rbioc/rbioc.job

Docker

Build the Docker container locally:

docker buildx create --use
#docker buildx build --load --platform linux/amd64,linux/arm64 -t ghcr.io/drejom/vscode-rbioc:latest
docker buildx build --load --platform linux/amd64 -t ghcr.io/drejom/vscode-rbioc:latest --progress=plain . 2>&1 | tee build.log

Get a shell locally:

docker run -it --rm ghcr.io/drejom/vscode-rbioc:latest /bin/bash