docker

Docker

Build the image from the repository root:

docker build -f docker/Dockerfile -t hcocena .

The image includes:

• the local hcocena package installation
• a ready-to-use workspace directly at /home/rstudio
• TB-neo-specific 01_hcocena_main.Rmd and 02_hcocena_satellite.Rmd
• a bundled /home/rstudio/reference_files folder with pathway, GO, hallmark, TF, and immune helper references
• an empty /home/rstudio/project_data folder with instructions for adding the project-specific .rds inputs yourself
• workflow notebooks directly in the workspace root: 01_hcocena_main.Rmd, 02_hcocena_satellite.Rmd, 03_hcocena_main_seq_only.Rmd
• preinstalled optional packages for common workflows, including graphlayouts, ellmer, DESeq2, limma, sva, edgeR, tximport, apeglm, ashr, EnhancedVolcano, pheatmap, org.Hs.eg.db, org.Mm.eg.db, CALIBERrfimpute, RCy3, SpatialExperiment, and GSVA
• empty count_data, annotation_data, and output directories

RStudio Server is exposed on port 8787 by the base image.

Updating the Docker Hub description

When publishing a new public Docker tag, update the overview file from the repository root with:

Rscript docker/update_dockerhub_overview.R <new-tag>

This updates DOCKERHUB_OVERVIEW.md so the new tag becomes the recommended pinned version and moves the previous recommended tag into the older reproducibility list. The docker pull / docker run quick start examples intentionally stay on latest, so the Docker Hub page still points to the current image even if the pinned-version text is not copied right away.

If Docker Hub is not syncing this file automatically, copy the updated markdown to the repository Overview field there right after pushing the new tag.