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c75526e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | # Docker Best Practices for Bioinformatics
## Multi-stage Builds
### Optimized Python Environment
```dockerfile
# 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
```dockerfile
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
```dockerfile
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
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