data/docs_cache/docker_docs.md

Docker Best Practices for Bioinformatics

Multi-stage Builds

Optimized Python Environment

# Build stage
FROM python:3.9-slim as builder
WORKDIR /build
COPY requirements.txt .
RUN pip install --no-cache-dir --user -r requirements.txt

# Production stage
FROM python:3.9-slim
COPY --from=builder /root/.local /root/.local
RUN apt-get update && apt-get install -y procps
WORKDIR /app

Bioinformatics Stack

FROM python:3.9-slim

RUN apt-get update && apt-get install -y --no-install-recommends \
    libhdf5-dev \
    libblas-dev \
    liblapack-dev \
    && rm -rf /var/lib/apt/lists/*

RUN pip install --no-cache-dir \
    scanpy>=1.9.0 \
    anndata>=0.8.0 \
    pandas>=1.5.0 \
    numpy>=1.21.0

WORKDIR /app

OpenProblems Compatible Container

FROM python:3.9-slim

RUN apt-get update && apt-get install -y procps
RUN pip install --no-cache-dir scanpy anndata pandas numpy

# Create non-root user for Nextflow
RUN groupadd -g 1000 nextflow && \
    useradd -u 1000 -g nextflow nextflow

USER nextflow
WORKDIR /app
ENTRYPOINT ["python"]

Best Practices

• Use specific versions for reproducibility
• Use minimal base images
• Create non-root users
• Combine RUN commands to reduce layers
• Use health checks for services
• Set appropriate resource limits