OmniBioAI Tool Images

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

100 SIF images · 64G total · ARM64 (aarch64)

Structure

omnibioai-tool-images/
├── dockerfiles/          ← one Dockerfile per tool
├── sif/                  ← built Singularity SIF images (gitignored)
├── build_logs/           ← build output logs (gitignored)
├── tests/                ← pytest test suite (97% coverage)
└── build_all.sh          ← build script

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.example.yaml
4. Restart TES — done!

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Tools Available (100 total)

Bio Core (10)

Tool	Image	Size
fastqc	sif/fastqc_arm64.sif	304M
multiqc	sif/multiqc_arm64.sif	658M
trimmomatic	sif/trimmomatic_arm64.sif	282M
samtools	sif/samtools_arm64.sif	76M
bcftools	sif/bcftools_arm64.sif	87M
bwa	sif/bwa_arm64.sif	83M
star	sif/star_arm64.sif	73M
featurecounts	sif/featurecounts_arm64.sif	76M
gatk	sif/gatk_arm64.sif	989M
deseq2	sif/deseq2_arm64.sif	461M

Variant Analysis (10)

Tool	Image	Size
vcftools	sif/vcftools_arm64.sif	89M
snpeff	sif/snpeff_arm64.sif	345M
vep	sif/vep_arm64.sif	602M
plink	sif/plink_arm64.sif	88M
freebayes	sif/freebayes_arm64.sif	73M
strelka2	sif/strelka2_arm64.sif	235M
gatk (mutect2)	sif/gatk_arm64.sif	reused
bcftools (filter)	sif/bcftools_arm64.sif	reused
plink (gwas)	sif/plink_arm64.sif	reused
vcftools (filter)	sif/vcftools_arm64.sif	reused

RNA-seq (10)

Tool	Image	Size
kallisto	sif/kallisto_arm64.sif	77M
salmon	sif/salmon_arm64.sif	76M
hisat2	sif/hisat2_arm64.sif	102M
stringtie	sif/stringtie_arm64.sif	88M
rsem	sif/rsem_arm64.sif	386M
edger	sif/edger_arm64.sif	390M
limma	sif/limma_arm64.sif	390M
dexseq	sif/dexseq_arm64.sif	526M
rmats	sif/rmats_arm64.sif	349M
tximport	sif/tximport_arm64.sif	377M

Metagenomics (10)

Tool	Image	Size
kraken2	sif/kraken2_arm64.sif	118M
bracken	sif/bracken_arm64.sif	85M
metaphlan	sif/metaphlan_arm64.sif	487M
humann3	sif/humann3_arm64.sif	807M
diamond	sif/diamond_arm64.sif	75M
prodigal	sif/prodigal_arm64.sif	73M
prokka	sif/prokka_arm64.sif	633M
checkm	sif/checkm_arm64.sif	406M
quast	sif/quast_arm64.sif	283M
spades	sif/spades_arm64.sif	85M

Epigenomics (10)

Tool	Image	Size
bismark	sif/bismark_arm64.sif	101M
macs2	sif/macs2_arm64.sif	85M
deeptools	sif/deeptools_arm64.sif	460M
homer	sif/homer_arm64.sif	101M
atacqc	sif/atacqc_arm64.sif	1.4G
chromhmm	sif/chromhmm_arm64.sif	285M
epic2	sif/epic2_arm64.sif	85M
bedtools	sif/bedtools_arm64.sif	73M
bismark (extractor)	sif/bismark_arm64.sif	reused
deeptools (matrix)	sif/deeptools_arm64.sif	reused

Single-cell (9)

Tool	Image	Size
seurat	sif/seurat_arm64.sif	559M
harmony	sif/harmony_arm64.sif	566M
monocle3	sif/monocle3_arm64.sif	462M
scrublet	sif/scrublet_arm64.sif	632M
scenic	sif/scenic_arm64.sif	750M
signac	sif/signac_arm64.sif	616M
doubletfinder	sif/doubletfinder_arm64.sif	563M
velocyto	sif/velocyto_arm64.sif	—
cellranger	⚠️ needs 10x license	—

Proteomics (10)

Tool	Image	Size
msfragger	sif/msfragger_arm64.sif	⚠️ needs license
flashlfq	sif/flashlfq_arm64.sif	138M
percolator	sif/percolator_arm64.sif	—
philosopher	sif/philosopher_arm64.sif	97M
maxquant	sif/maxquant_arm64.sif	314M
moff	sif/moff_arm64.sif	—
ionquant	sif/ionquant_arm64.sif	493M
skyline	sif/skyline_arm64.sif	300M
fragpipe	sif/fragpipe_arm64.sif	—
tpp	sif/tpp_arm64.sif	300M

Structural Biology (10)

Tool	Image	Size
autodock	sif/autodock_arm64.sif	201M
pymol	sif/pymol_arm64.sif	183M
rosetta	sif/rosetta_arm64.sif	200M
gromacs	sif/gromacs_arm64.sif	162M
openmm	sif/openmm_arm64.sif	262M
modeller	sif/modeller_arm64.sif	200M
hmmer	sif/hmmer_arm64.sif	75M
pdbfixer	sif/pdbfixer_arm64.sif	262M
muscle	sif/muscle_arm64.sif	72M
iqtree	sif/iqtree_arm64.sif	76M

ML / AI (10)

Tool	Image	Size
pytorch	sif/pytorch_arm64.sif	5.7G
tensorflow	sif/tensorflow_arm64.sif	884M
huggingface	sif/huggingface_arm64.sif	5.8G
sklearn	sif/sklearn_arm64.sif	407M
xgboost	sif/xgboost_arm64.sif	1.4G
rapids	sif/rapids_arm64.sif	498M
esm2	sif/esm2_arm64.sif	5.6G
alphafold2	sif/alphafold2_arm64.sif	6.5G
cellpose	sif/cellpose_arm64.sif	5.9G
scanpy	sif/scanpy_arm64.sif	621M

More Bioinformatics (11)

Tool	Image	Size
busco	sif/busco_arm64.sif	85M
minimap2	sif/minimap2_arm64.sif	76M
medaka	sif/medaka_arm64.sif	88M
nanostat	sif/nanostat_arm64.sif	315M
flye	sif/flye_arm64.sif	85M
repeatmasker	sif/repeatmasker_arm64.sif	99M
trinity	sif/trinity_arm64.sif	101M
transdecoder	sif/transdecoder_arm64.sif	83M
interproscan	sif/interproscan_arm64.sif	5.8G
orthofinder	sif/orthofinder_arm64.sif	88M
augustus	sif/augustus_arm64.sif	116M

Population Genetics / GWAS (12)

Tool	Image	Size
admixture	sif/admixture_arm64.sif	74M
eigensoft	sif/eigensoft_arm64.sif	262M
beagle	sif/beagle_arm64.sif	282M
shapeit	sif/shapeit_arm64.sif	335M
gcta	sif/gcta_arm64.sif	440M
ldsc	sif/ldsc_arm64.sif	405M
plink2	sif/plink2_arm64.sif	393M
regenie	sif/regenie_arm64.sif	355M
saige	sif/saige_arm64.sif	430M
metal	sif/metal_arm64.sif	212M
structure	sif/structure_arm64.sif	333M
impute2	sif/impute2_arm64.sif	74M

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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 — 64G 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