OmniBioAI Tool Images

ARM64-compatible Docker/Singularity images for bioinformatics and ML tools running on DGX Spark via Slurm.

1,000 SIF images built locally · 1,249 Dockerfiles defined · ARM64 (aarch64) (verified 2026-08-07 by direct file count; SIF count reflects this machine's local sif/ state, not a fixed platform-wide total)

Structure

omnibioai-tool-images/
├── dockerfiles/          ← 1,249 Dockerfiles, one per tool
├── api/
│   └── server.py         ← Build/status API — see "API" below
├── frontend/tool-images-ui/  ← React + TypeScript UI (Vite) — see "Frontend" below
├── sif/                  ← built Singularity SIF images (gitignored)
├── build_logs/           ← build output logs (gitignored)
├── tests/                ← pytest test suite (coverage configured at 95% minimum)
├── build_all.sh          ← build all images
└── build_missing_sifs.sh ← rebuild only missing/failed SIFs

Quick Start

# Build a single tool
bash build_all.sh fastqc

# Build all tools
bash build_all.sh

# Build selected missing tools with the fallback builder
bash build_new_tools.sh tool_a tool_b

# Run tests
pytest tests/ -v -k "not test_tool_runs_in_sif"

Add a New Tool

1. Write dockerfiles/Dockerfile.toolname
2. Run bash build_all.sh toolname
3. Add tool entry to omnibioai-tes/configs/tools/<domain>.yaml (edit the appropriate category file)
4. Run make restart in omnibioai-tes — done!

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Tools Available (29 domains)

Tool configurations live in omnibioai-tes/configs/tools/ — one YAML file per domain. Per-domain counts below sum to 1,007 and were not independently re-verified in this pass — they may lag the 1,249 real Dockerfiles and 1,000 built SIFs above; treat the per-domain breakdown as directional, not exact.

#	Domain	Config file	Tools	Examples
01	QC & Preprocessing	01_qc_preprocessing.yaml	35	FastQC, MultiQC, Trimmomatic
02	Alignment	02_alignment.yaml	31	BWA-MEM, BLASTN, Samtools
03	RNA-seq	03_rnaseq.yaml	58	DESeq2, Kallisto, featureCounts
04	Variant Analysis	04_variants.yaml	57	GATK, BCFtools, VEP
05	Epigenomics	05_epigenomics.yaml	36	Bismark, MACS2, deepTools
06	Single-cell	06_single_cell.yaml	45	Seurat, Scanpy, Cell Ranger
07	Spatial Omics	07_spatial.yaml	11	Cellpose, Space Ranger, Squidpy
08	Assembly	08_assembly.yaml	20	SPAdes, Flye, QUAST
09	Metagenomics	09_metagenomics.yaml	30	Kraken2, MetaPhlAn, HUMAnN3
10	Microbiome	10_microbiome.yaml	18	QIIME2, nf-core Ampliseq
11	Population Genetics	11_population_genetics.yaml	29	ADMIXTURE, GCTA, REGENIE
12	Structural Biology	12_structural_biology.yaml	27	AlphaFold2, AutoDock, ESM-2
13	Immunogenomics	13_immunogenomics.yaml	6	MiXCR, TRUST4, arcasHLA
14	Ancient DNA	14_ancient_dna.yaml	1	EAGER2
15	Metabolomics	15_metabolomics.yaml	5	XCMS, MZmine3, SIRIUS
16	Drug Discovery	16_drug_discovery.yaml	1	ADMET Prediction
17	Proteomics	17_proteomics.yaml	14	MSFragger, Percolator, Philosopher
18	ML / DL	18_ml_dl.yaml	19	PyTorch, TensorFlow, RAPIDS
19	Cancer Genomics	19_cancer_genomics.yaml	10	AMBER, COBALT, Survival KM
20	Comparative Genomics	20_comparative_genomics.yaml	8	OrthoFinder, MCScan
21	Multi-omics	21_multiomics.yaml	4	MOFA+, MOSCOT
22	Proteogenomics	22_proteogenomics.yaml	4	TransDecoder, PRICE, Xtail
23	nf-core Pipelines	23_nfcore_pipelines.yaml	2	nf-core RNA-seq, Nanoseq
24	Annotation	24_annotation.yaml	4	RepeatMasker, AUGUSTUS, DAVID
25	Genomic Utilities	25_genomic_utilities.yaml	3	BEDTools, BEDOPS, PyMOL
26	Long Read	26_longread.yaml	6	Guppy, Dorado, Medaka
27	CRISPR	27_crispr.yaml	9	MAGeCK, Cas-OFFinder
28	Imaging	28_imaging.yaml	2	Steinbock, MCMICRO
29	HTTP Tools	29_http_tools.yaml	512	Enrichr, OmniBioAI Workflow Runner

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Testing

# Run all tests (excluding live SIF execution)
pytest tests/ -v -k "not test_tool_runs_in_sif"

# Run with coverage
pytest tests/ --cov=scripts --cov-report=term-missing \
  -k "not test_tool_runs_in_sif"

# Run including SIF execution tests (requires Singularity)
pytest tests/ -v

Historical test result (verified 2026-08-07): 10,008 passed · 1,525 failed · 1 skipped in 31s (excludes live SIF-execution tests). The failures were all one category — test_dockerfiles.py::TestDockerfileStructure::test_dockerfile_uses_approved_base, parametrized per tool (yak, yara, zarr_extra, zarr_v2_extra, and many more) — a base-image policy check a large number of Dockerfiles currently fail, not 1,525 independent issues. Not investigated further here (README-only pass); flagging honestly rather than repeating the stale "1026 passed" figure, which predates this.

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API

api/server.py (FastAPI) serves as the tool-images container in omnibioai-studio's compose stack, port 8097.

Method	Endpoint	Status
GET	/health	Working
GET	/v1/tools	Working — lists tools discovered from dockerfiles/Dockerfile.*
GET	/v1/tools/{tool}/dockerfile	Working — returns the raw Dockerfile
GET	/v1/tools/{tool}/log	Working — returns the build log if one exists
POST	/v1/build/{tool}	Known non-functional (documented in code, issue #13, closed won't-fix)
POST	/v1/build-all	Known non-functional (same reason)

The two build endpoints shell out to build_all.sh, but the container this API runs in only has api/ copied into it — no Docker CLI, no /var/run/docker.sock, no Singularity/Apptainer binary, and build_all.sh itself isn't even present in the image. They're left in place returning exit 127 rather than reworked into something that looks functional but isn't. The real build path is host-side: build_missing_sifs.sh (or build_all.sh directly), run on a host with Docker + Singularity installed — never through this HTTP API.

The API container exposes two ports in the Compose deployment:

• 8097 — FastAPI API (/health, /v1/*, and /docs)
• 5179 — nginx-served React frontend, proxying /v1/* to the API

The standalone Docker image copies the API and frontend only. Compose mounts the host dockerfiles/, sif/, and build_logs/ directories into the container so the UI can inspect the current host-side build state.

Frontend

frontend/tool-images-ui/ (React + TypeScript, Vite) — ships in this same repo, not documented elsewhere.

cd frontend/tool-images-ui
npm install
npm run dev

The production frontend is served by nginx on port 5179. The Vite development server uses its own development port and is useful when working on the UI independently of the Compose container.

Notes

• All images are built for linux/arm64 (aarch64) — DGX Spark / Grace Hopper
• build_all.sh, build_missing_sifs.sh, and the fallback builders are ARM64 workflows; build_multiarch_sifs.sh is the separate workflow for its explicitly selected amd64 + arm64 tool set
• SIF files are stored in sif/ (gitignored — ~235G total)
• Tools marked ⚠️ require an external license or manual download
• Tools reusing an existing SIF are noted as reused
• Build logs are in build_logs/ (gitignored)

Requirements

For host-side image/SIF builds, install:

• Python 3.11 or newer
• Docker with BuildKit/buildx support
• Singularity or Apptainer
• Sufficient local storage for Docker layers, build logs, and SIF images

For the frontend, use Node.js/npm. The API container installs its Python runtime dependencies during the Docker build; host-side test execution uses the dependencies in requirements-test.txt and the coverage configuration in pyproject.toml.

Related Repos

Repo	Description
omnibioai-tes	Tool Execution Service — orchestrates Slurm jobs
omnibioai-tool-runtime	Containerized tool runner
omnibioai	Main Django application
omnibioai-toolserver	HTTP ToolServer shim