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author galaxytrakr
date Fri, 25 Sep 2026 20:13:08 +0000
parents c449145d54cb
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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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23 # ============================================================================
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24 # Stage 2: Builder - Install all dependencies and SeqSero2S
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25 # ============================================================================
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26 FROM base AS builder
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27
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28 # Update base packages and install build essentials
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29 RUN apt-get update && \
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30 apt-get install -y --no-install-recommends \
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31 wget \
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32 ca-certificates \
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33 bash \
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34 && apt-get clean && \
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35 rm -rf /var/lib/apt/lists/*
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36
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37 # Create conda environment with all dependencies
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38 # Using mamba for faster dependency resolution
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39 RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
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40 python>=3 \
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41 pip \
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42 setuptools \
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43 blast>=2.2 \
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44 zstd \
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45 samtools \
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46 bedtools>=2.17 \
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47 sra-tools>=2.8 \
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48 spades>=3.9 \
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49 salmid \
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50 bwa>=0.7 \
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51 seqtk>=1.3 \
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52 stringmlst>=0.6 \
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53 perl-list-moreutils \
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54 && mamba create -n mlst_env -c conda-forge -c bioconda \
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55 mlst>=2.32 \
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56 && mamba clean -afy
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60 # Install SeqSero2S from local fork
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61 WORKDIR /tmp/build/SeqSero2S
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62
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63 # Copy the current build context (the cloned source code) into the container.
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64 COPY . .
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65
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66 # Install SeqSero2S
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67 RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
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68
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69 # Apply the stringMLST.py patch inline using 'sed'.
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70 # This exactly replicates the original python patch script by commenting out the old line and adding the new one.
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71 RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \
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72 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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73 echo "PATCHED: stringMLST.py log path fixed"; \
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74 else \
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75 echo "SKIP: stringMLST.py not found"; \
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76 fi
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77
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78 # ============================================================================
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79 # Stage 3: Test image - runs validation tests
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80 # ============================================================================
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81 FROM builder AS test
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82
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83 # Create test directory
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84 WORKDIR /test
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85
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86 # Run test commands from the conda recipe
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87 RUN echo "Running SeqSero2S tests..." && \
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88 /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
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89 echo "SeqSero2S.py -h: PASSED" && \
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90 /opt/conda/envs/seqsero2s/bin/blastn -help && \
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91 echo "blastn -help: PASSED" && \
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92 /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
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93 echo "SalmID.py -h: PASSED" && \
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94 /opt/conda/envs/mlst_env/bin/mlst -h && \
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95 echo "mlst -h: PASSED" && \
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96 echo "All tests completed successfully!"
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97
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98 # Default command shows test results
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99 CMD ["echo", "All SeqSero2S tests passed successfully!"]
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100
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101 # ============================================================================
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102 # Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
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103 # ============================================================================
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104 FROM condaforge/mambaforge:latest AS dist
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105
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106 # Copy conda environment from builder
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107 COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
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108 COPY --from=builder /opt/conda/envs/mlst_env /opt/conda/envs/mlst_env
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109
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110 # Update PATH to use the conda environment
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111 ENV PATH=/opt/conda/envs/mlst_env/bin:/opt/conda/envs/seqsero2s/bin:$PATH \
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112 CONDA_DEFAULT_ENV=seqsero2s \
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113 CONDA_PREFIX=/opt/conda/envs/seqsero2s
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114
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115 # Install minimal runtime dependencies
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116 RUN apt-get update && \
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117 apt-get install -y --no-install-recommends \
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118 ca-certificates \
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119 procps \
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120 && apt-get clean && \
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121 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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122
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123 # Create working directory
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124 WORKDIR /data
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125
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126 # Create non-root user for running the application
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127 RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
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128 chown -R seqsero2s:seqsero2s /data
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129 USER seqsero2s
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130
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131 # Add metadata labels
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132 LABEL org.opencontainers.image.version="1.1.4" \
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133 org.opencontainers.image.authors="LSTUGA" \
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134 org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
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135 org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
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136 org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
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137 org.opencontainers.image.licenses="GPL-2.0-or-later" \
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138 org.opencontainers.image.title="SeqSero2S" \
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139 org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
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140
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141 # No entrypoint or command for dist target
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142
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143