omnibioai/omnibioai-sif-images
OmniBioAI SIF Images 🧬 500+ native ARM64 Singularity (SIF) container images for bioinformatics, built on NVIDIA DGX (aarch64). Tool Categories Category Tools Genomics & Alignment BWA, STAR, HISAT2, Minimap2, Bowtie2 Variant Calling GATK, DeepVariant, Clair3, Mutect2 RNA-seq Salmon, Kallisto, DESeq2, edgeR Single Cell Seurat, Scanpy, Cell Ranger, Harmony Epigenomics MACS2, deepTools, Bismark Metagenomics Kraken2, MetaPhlAn, QIIME2 Proteomics… See the full description on the dataset page: https://huggingface.co/datasets/omnibioai/omnibioai-sif-images.
018k
1Bootstrap: docker2From: python:3.12-slim3 4%labels5 Author OmniBioAI6 Version 2.07 Description BioQueryAI full bioinformatics sandbox for LLM-generated scripts8 9%post10 apt-get update && apt-get install -y --no-install-recommends \11 gcc g++ make cmake \12 zlib1g-dev libbz2-dev liblzma-dev \13 libcurl4-openssl-dev libssl-dev \14 libhts-dev \15 samtools bcftools tabix \16 bedtools \17 wget curl git procps \18 && apt-get clean && rm -rf /var/lib/apt/lists/*19 20 pip install --no-cache-dir --upgrade pip setuptools wheel21 pip install --no-cache-dir "pandas>=2.2,<3" "numpy>=1.26,<2" "scipy>=1.13,<2" "statsmodels>=0.14,<1" "scikit-learn>=1.5,<2" "matplotlib>=3.9,<4" "seaborn>=0.13,<1" "plotly>=5.22,<6"22 pip install --no-cache-dir "pysam>=0.22,<1" "cyvcf2>=0.31,<1" "biopython>=1.84,<2" "pybedtools>=0.10,<1"23 pip install --no-cache-dir "anndata>=0.10,<1" "scanpy>=1.10,<2"24 pip install --no-cache-dir "pydeseq2>=0.4,<1"25 pip install --no-cache-dir "gseapy>=1.1,<2"26 pip install --no-cache-dir "lifelines>=0.29,<1"27 pip install --no-cache-dir "networkx>=3.3,<4"28 pip install --no-cache-dir tqdm openpyxl xlrd pyarrow pyyaml tabulate rich29 30 mkdir -p /workspace/inputs /workspace/figures /workspace/tables /workspace/text /workspace/files /workspace/logs /workspace/meta31 32%environment33 export PYTHONUNBUFFERED=134 export MPLBACKEND=Agg35 export HOME=/tmp36 export PIP_NO_CACHE_DIR=137 38%runscript39 exec python "$@"40 41%test42 python -c "43packages = ['pandas','numpy','scipy','matplotlib','seaborn','sklearn','statsmodels','networkx','lifelines','gseapy','anndata','scanpy','pydeseq2','Bio','pysam','cyvcf2','pybedtools']44ok, fail = [], []45for p in packages:46 try: __import__(p); ok.append(p)47 except Exception as e: fail.append(f'{p}: {e}')48print('OK:', ok)49if fail: print('FAILED:', fail)50else: print('BioQueryAI sandbox ready.')51"52