OmniBioAI Tool Images

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

459 SIF images · ~235G total · ARM64 (aarch64)

Structure

omnibioai-tool-images/
├── dockerfiles/          ← 454 Dockerfiles, one per tool
├── 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 (459 SIF images · 29 domains)

Tool configurations live in omnibioai-tes/configs/tools/ — one YAML file per domain.

#	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: 1026 passed · 97% coverage · 2.45s

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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