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author jpayne
date Fri, 15 May 2026 17:50:45 +0000
parents 790b6c0e71fb
children 6041d8f4eeeb
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1 # Multi-stage Dockerfile for SeqSero2S
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2 # Default build: docker build -t seqsero2s:latest .
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3 # Test build: docker build --target test -t seqsero2s:test .
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4
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5 # ============================================================================
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6 # Stage 1: Base image with mambaforge for faster dependency resolution
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7 # ============================================================================
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8 FROM condaforge/mambaforge:latest AS base
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9
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10 LABEL maintainer="SeqSero2S Maintainers"
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11 LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"
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12
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13 # Set environment variables to reduce conda output and ensure non-interactive
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14 # Disable SSL verification for VPN environments
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15 ENV CONDA_ALWAYS_YES=true \
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16 CONDA_AUTO_UPDATE_CONDA=false \
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17 DEBIAN_FRONTEND=noninteractive
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18
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19 # Configure conda to skip SSL verification
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20 RUN conda config --set ssl_verify false
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21
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22 # ============================================================================
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23 # Stage 2: Builder - Install all dependencies and SeqSero2S
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24 # ============================================================================
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25 FROM base AS builder
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26
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27 # Update base packages and install build essentials
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28 RUN apt-get update && \
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29 apt-get install -y --no-install-recommends \
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30 wget \
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31 ca-certificates \
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32 bash \
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33 && apt-get clean && \
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34 rm -rf /var/lib/apt/lists/*
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35
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36 # Create conda environment with all dependencies
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37 # Using mamba for faster dependency resolution
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38 RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
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39 python>=3 \
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40 pip \
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41 setuptools \
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42 blast>=2.2 \
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43 zstd \
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44 samtools \
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45 bedtools>=2.17 \
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46 sra-tools>=2.8 \
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47 spades>=3.9 \
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48 salmid \
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49 bwa>=0.7 \
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50 seqtk>=1.3 \
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51 stringmlst>=0.6 \
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52 mlst>=2.32.2 \
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53 perl-list-moreutils \
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54 && mamba clean -afy
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55
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56 # Install SeqSero2S from local fork
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57 WORKDIR /tmp/build/SeqSero2S
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58
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59 # Copy the current build context (the cloned source code) into the container.
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60 COPY . .
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61
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62 # Install SeqSero2S
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63 RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
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64
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65 # Apply the stringMLST.py patch inline using 'sed'.
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66 # This exactly replicates the original python patch script by commenting out the old line and adding the new one.
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67 RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \
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68 sed -i 's| log = dbPrefix+'\''.log'\''| # log = dbPrefix+'\''.log'\''\n log = os.path.join(os.getcwd(), "kmer.log")|g' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \
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69 echo "PATCHED: stringMLST.py log path fixed"; \
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70 else \
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71 echo "SKIP: stringMLST.py not found"; \
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72 fi
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73
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74 # ============================================================================
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75 # Stage 3: Test image - runs validation tests
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76 # ============================================================================
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77 FROM builder AS test
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78
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79 # Create test directory
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80 WORKDIR /test
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81
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82 # Run test commands from the conda recipe
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83 RUN echo "Running SeqSero2S tests..." && \
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84 /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
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85 echo "SeqSero2S.py -h: PASSED" && \
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86 /opt/conda/envs/seqsero2s/bin/blastn -help && \
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87 echo "blastn -help: PASSED" && \
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88 /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
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89 echo "SalmID.py -h: PASSED" && \
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90 /opt/conda/envs/seqsero2s/bin/mlst -h && \
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91 echo "mlst -h: PASSED" && \
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92 echo "All tests completed successfully!"
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93
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94 # Default command shows test results
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95 CMD ["echo", "All SeqSero2S tests passed successfully!"]
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96
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97 # ============================================================================
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98 # Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
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99 # ============================================================================
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100 FROM condaforge/mambaforge:latest AS dist
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101
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102 # Copy conda environment from builder
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103 COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
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104
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105 # Update PATH to use the conda environment
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106 ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \
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107 CONDA_DEFAULT_ENV=seqsero2s \
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108 CONDA_PREFIX=/opt/conda/envs/seqsero2s
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109
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110 # Install minimal runtime dependencies
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111 RUN apt-get update && \
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112 apt-get install -y --no-install-recommends \
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113 ca-certificates \
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114 procps \
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115 && apt-get clean && \
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116 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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117
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118 # Create working directory
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119 WORKDIR /data
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120
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121 # Create non-root user for running the application
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122 RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
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123 chown -R seqsero2s:seqsero2s /data
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124 USER seqsero2s
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125
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126 # Add metadata labels
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127 LABEL org.opencontainers.image.version="1.1.4" \
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128 org.opencontainers.image.authors="LSTUGA" \
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129 org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
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130 org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
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131 org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
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132 org.opencontainers.image.licenses="GPL-2.0-or-later" \
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133 org.opencontainers.image.title="SeqSero2S" \
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134 org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
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135
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136 # No entrypoint or command for dist target
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137
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138