Mercurial > repos > jpayne > seqsero2s

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author galaxytrakr
date Fri, 15 May 2026 11:48:22 +0000
parents 4c4899031795
children b91011f3b337
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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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9
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6 # ============================================================================
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7 # Stage 1: Base image with mambaforge for faster dependency resolution
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8 # ============================================================================
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9 FROM condaforge/mambaforge:latest AS base
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10
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11 LABEL maintainer="SeqSero2S Maintainers"
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12 LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"
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13
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14 # Set environment variables to reduce conda output and ensure non-interactive
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15 # Disable SSL verification for VPN environments
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16 ENV CONDA_ALWAYS_YES=true \
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17 CONDA_AUTO_UPDATE_CONDA=false \
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18 DEBIAN_FRONTEND=noninteractive
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19
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20 # Configure conda to skip SSL verification
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21 RUN conda config --set ssl_verify false
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22
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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 # Copy the patch script
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38 COPY patch_stringmlst.sh /tmp/patch_stringmlst.sh
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39 RUN chmod +x /tmp/patch_stringmlst.sh
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40
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41 # Create conda environment with all dependencies
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42 # Using mamba for faster dependency resolution
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43 RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
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44 python>=3 \
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45 pip \
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46 setuptools \
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47 blast>=2.2 \
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48 zstd \
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49 samtools \
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50 bedtools>=2.17 \
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51 sra-tools>=2.8 \
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52 spades>=3.9 \
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53 salmid \
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54 bwa>=0.7 \
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55 seqtk>=1.3 \
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56 stringmlst>=0.6 \
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57 mlst>=2.32.2 \
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58 perl-list-moreutils \
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59 && mamba clean -afy
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60
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61 # Install SeqSero2S from local fork
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62 WORKDIR /tmp/build
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63
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64 # Copy local SeqSero2S directory
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65 COPY SeqSero2S /tmp/build/SeqSero2S
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66
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67 # Install SeqSero2S
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68 RUN cd SeqSero2S && \
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69 /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
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70
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71 # Apply the stringMLST.py patch (from the conda recipe)
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72 # The patch replaces dbPrefix reference with cwd to avoid path issues
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73 RUN PREFIX=/opt/conda/envs/seqsero2s /tmp/patch_stringmlst.sh
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74
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75 # ============================================================================
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76 # Stage 3: Test image - runs validation tests
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77 # ============================================================================
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78 FROM builder AS test
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79
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80 # Create test directory
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81 WORKDIR /test
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82
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83 # Run test commands from the conda recipe
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84 RUN echo "Running SeqSero2S tests..." && \
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85 /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
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86 echo "SeqSero2S.py -h: PASSED" && \
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87 /opt/conda/envs/seqsero2s/bin/blastn -help && \
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88 echo "blastn -help: PASSED" && \
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89 /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
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90 echo "SalmID.py -h: PASSED" && \
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91 /opt/conda/envs/seqsero2s/bin/mlst -h && \
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92 echo "mlst -h: PASSED" && \
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93 echo "All tests completed successfully!"
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94
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95 # Default command shows test results
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96 CMD ["echo", "All SeqSero2S tests passed successfully!"]
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97
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98 # ============================================================================
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99 # Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
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100 # ============================================================================
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101 FROM condaforge/mambaforge:latest AS dist
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102
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103 # Copy conda environment from builder
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104 COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
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105
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106 # Update PATH to use the conda environment
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107 ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \
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108 CONDA_DEFAULT_ENV=seqsero2s \
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109 CONDA_PREFIX=/opt/conda/envs/seqsero2s
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110
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111 # Install minimal runtime dependencies
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112 RUN apt-get update && \
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113 apt-get install -y --no-install-recommends \
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114 ca-certificates \
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115 procps \
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116 && apt-get clean && \
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117 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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118
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119 # Create working directory
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120 WORKDIR /data
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121
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122 # Create non-root user for running the application
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123 RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
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124 chown -R seqsero2s:seqsero2s /data
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125
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126 USER seqsero2s
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127
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128 # Add metadata labels
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129 LABEL org.opencontainers.image.version="1.1.4" \
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130 org.opencontainers.image.authors="LSTUGA" \
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131 org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
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132 org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
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133 org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
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134 org.opencontainers.image.licenses="GPL-2.0-or-later" \
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135 org.opencontainers.image.title="SeqSero2S" \
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136 org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
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137
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138 # No entrypoint or command for dist target