biodepot_baseimages

Dockerfiles for BioDepot base images that don't belong to a specific BWB widget. The curated analysis tiers live in BioDepot/bwb-bioc-images; this repo is the layer below — R, Bioc, Jupyter, Dorado — plus historical references.

Layout

biodepot_baseimages/
├── r/                source-built R with explicit BLAS/LAPACK
├── bioc-r/           Bioconductor+R — two build paths, see bioc-r/README.md
├── jupyter-base/     Jupyter + Python+R (non-Bioc)
├── jupyter-bioc-r/   Jupyter + IRkernel on bioc-r — two build paths
└── dorado/           GPU basecaller image

The two-path policy (bioc-r and jupyter-bioc-r)

For Bioconductor-flavored images we maintain two parallel build lineages per release:

• Primary (community path) — builds FROM bioconductor/bioconductor_docker:RELEASE_X_Y. Tag: biodepot/bioc-r:RELEASE_X_Y. Fast to build, small, tracks the upstream community image.
• Fallback (source-build path) — builds FROM BioDepot's own biodepot/rbase (source-compiled R with explicit BLAS/LAPACK). Tag: biodepot/bioc-r:RELEASE_X_Y-source. Slower (~30 min R compile), owned end-to-end by BioDepot.

Both variants are built and pushed on every Bioc release bump. The -source suffix is not a fallback-of-last-resort — it's a first-class published image that workflows can pin to.

See bioc-r/README.md for when to reach for each path.

Related repositories

• BioDepot/bwb-bioc-images — curated Bioc tier images (bulk-RNA, single-cell, conversion bridges). Built FROM bioconductor/bioconductor_docker directly today; may layer on biodepot/bioc-r in a future refactor.
• BioDepot/biodepot-tools — Perl orchestration for widget-level Dockerfiles.
• BioDepot/BioDepot-workflow-builder (BWB) — widget-per-Dockerfile repo; its images are separate from this chain.

Bioconductor release cadence

Bioconductor publishes twice yearly (spring + fall). On each release:

1. Update the release pin in bioc-r/<X.Y>/Dockerfile and the -source variant.
2. Build both bioc-r variants; verify smoke test.
3. Build both jupyter-bioc-r variants; verify smoke test.
4. Push all four; file a PR to the catalog (biodepot-catalog) updating digests.

The update-agent skill at ~/.claude/skills/bioc-module-update/ encodes this procedure.

Historical note on r/ + bioc-r/-source

The r/ tier exists for Python+R Jupyter workflows that don't need Bioconductor, and as the source-build dependency for the bioc-r -source variant. If the community Bioc path is ever broken, biodepot/rbase + bioc-r/-source is a fully BioDepot-owned escape hatch. This is deliberate, not vestigial.