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 (33 more under obsolete/)
├── 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 (97% coverage)
├── 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 in parallel (N workers)
bash build_all.sh --parallel 4

# 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=tests --cov-report=term-missing \
  -k "not test_tool_runs_in_sif"

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

Test results (verified 2026-08-07): 10,008 passed · 1,525 failed · 1 skipped in 31s (excludes live SIF-execution tests). The failures are 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.

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

Notes

• All images are built for linux/arm64 (aarch64) — DGX Spark / Grace Hopper
• 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)

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